Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0042626 ATPase-coupled transmembrane transporter activity	IBA GO_REF:0000033	ACCEPT	Summary: ABCD3 is an established ATP-dependent peroxisomal membrane transporter. IBA annotation is phylogenetically sound and well-supported by direct experimental data from proteoliposome reconstitution studies [PMID:29397936] and yeast complementation assays [PMID:24333844]. Reason: Core molecular function of ABCD3, supported by multiple lines of experimental evidence including ATPase activity measurements and substrate transport assays. Supporting Evidence: PMID:29397936 ABCD1-4 displayed stable ATPase activity, which was inhibited by AlF3 PMID:24333844 the phenotype of the pxa1/pxa2Delta yeast mutant, i.e. impaired oxidation of oleic acid, cannot only be partially rescued by HsABCD1, HsABCD2, but also by HsABCD3
GO:0005324 long-chain fatty acid transmembrane transporter activity	IBA GO_REF:0000033	ACCEPT	Summary: ABCD3 transports long-chain fatty acids across the peroxisomal membrane. Demonstrated by yeast complementation showing rescue of fatty acid oxidation defects [PMID:24333844] and supported by loss-of-function studies in knockout mice [PMID:34564857]. Reason: Core function. IBA annotation is well-supported by IMP evidence from van Roermund et al. showing ABCD3 can partially rescue oleic acid oxidation in yeast mutants. Supporting Evidence: PMID:24333844 most hydrophilic substrates like long-chain unsaturated-, long branched-chain- and long-chain dicarboxylic fatty acids by HsABCD3
GO:0005778 peroxisomal membrane	IBA GO_REF:0000033	ACCEPT	Summary: ABCD3 is a well-established peroxisomal membrane protein, demonstrated by immunofluorescence and FRET microscopy in multiple studies [PMID:17609205, PMID:17761678, PMID:10704444]. Reason: Core localization. Extensively validated by multiple experimental methods including immunofluorescence, FRET, and cryo-EM structures (PDB: 8Z0F, 8Z9X). Supporting Evidence: PMID:17609205 ALDP and PMP70 form homodimers as well as ALDP/PMP70 heterodimers
GO:0006635 fatty acid beta-oxidation	IBA GO_REF:0000033	ACCEPT	Summary: ABCD3 facilitates import of fatty acid substrates into peroxisomes for beta-oxidation. Supported by yeast complementation studies [PMID:24333844] and overexpression rescue of VLCFA beta-oxidation defects [PMID:9425230]. Reason: Core biological process. ABCD3 imports substrates destined for peroxisomal beta-oxidation. IBA is phylogenetically sound and experimentally validated. Supporting Evidence: PMID:24333844 the phenotype of the pxa1/pxa2Delta yeast mutant, i.e. impaired oxidation of oleic acid, cannot only be partially rescued by HsABCD1, HsABCD2, but also by HsABCD3 PMID:9425230 Expression of either ALDP or PMP70 restores VLCFA beta-oxidation in X-ALD fibroblasts, indicating overlapping functions
GO:0015910 long-chain fatty acid import into peroxisome	IBA GO_REF:0000033	ACCEPT	Summary: ABCD3 imports long-chain fatty acids into peroxisomes as CoA esters. Supported by yeast complementation [PMID:24333844] and ABCD3-deficient patient data [PMID:25168382]. Reason: Core function of ABCD3. Phylogenetically conserved and experimentally validated. Supporting Evidence: PMID:24333844 All these fatty acids are most likely transported as CoA esters
GO:0042760 very long-chain fatty acid catabolic process	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: ABCD3 contributes to VLCFA catabolism by importing substrates for peroxisomal beta-oxidation. Supported by IGI evidence from ABCD1/ABCD3 co-expression studies [PMID:9425230], though ABCD1 is the primary VLCFA transporter. Reason: ABCD3 contributes to VLCFA catabolism but is not the primary transporter for VLCFAs. ABCD1 preferentially handles the most hydrophobic VLCFAs (C24:0, C26:0) [PMID:24333844]. ABCD3 prefers more hydrophilic substrates. The Ferdinandusse et al. patient showed normal C26:0 beta-oxidation despite ABCD3 deficiency [PMID:25168382]. Supporting Evidence: PMID:25168382 Peroxisomal beta-oxidation of C26:0 was normal, but beta-oxidation of pristanic acid was reduced PMID:24333844 most hydrophobic C24:0 and C26:0 fatty acids are preferentially transported by HsABCD1
GO:0005524 ATP binding	IBA GO_REF:0000033	ACCEPT	Summary: ABCD3 binds ATP via its nucleotide binding fold. Directly demonstrated by purified NBF studies with KM of 8.2 uM for ATP [PMID:11248239]. Reason: Core function, essential for transport activity. Phylogenetically conserved ABC transporter feature with direct experimental validation. Supporting Evidence: PMID:11248239 Both proteins act as an ATP specific binding subunit releasing ADP after ATP hydrolysis
GO:0007031 peroxisome organization	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: ABCD3 overexpression can rescue peroxisome biogenesis defects in PEX2-deficient cells [PMID:9425230, PMID:9765053]. This likely reflects its role as a major peroxisomal membrane component rather than a direct organizer of peroxisome biogenesis. Reason: Not a core function. The effect on peroxisome organization is indirect, reflecting ABCD3's abundance in the peroxisomal membrane rather than a direct role in peroxisome biogenesis. Supporting Evidence: PMID:9425230 Their expression also restores peroxisome biogenesis in cells that are deficient in the peroxisomal membrane protein Pex2p
GO:0005739 mitochondrion	IEA GO_REF:0000107	REMOVE	Summary: IEA transfer from rat ortholog. ABCD3 is overwhelmingly established as a peroxisomal membrane protein. The N-terminal 80aa segment of PMP70, when expressed alone, can target to the outer mitochondrial membrane [PMID:20007743], but full-length PMP70 localizes exclusively to peroxisomes. This IEA annotation is misleading. Reason: ABCD3 is a peroxisomal protein. While an isolated N-terminal fragment can mis-target to mitochondria [PMID:20007743], this is an artifact of truncation, not physiological localization. No full-length ABCD3 has been demonstrated in mitochondria. Supporting Evidence: PMID:20007743 When the N80-segment was fused to EGFP, the fusion protein was targeted to the outer mitochondrial membrane... The full-length PMP70 molecule was clearly located in the ER in the absence of the N80-segment
GO:0006699 bile acid biosynthetic process	IEA GO_REF:0000107	ACCEPT	Summary: ABCD3 imports C27-bile acid intermediates into peroxisomes for side-chain shortening, a critical step in bile acid biosynthesis. Loss of ABCD3 causes CBAS5 with accumulation of C27-bile acid intermediates [PMID:25168382]. Reason: Well-supported by patient data and knockout mouse studies. ABCD3 transports bile acid CoA-esters (DHCA-CoA, THCA-CoA) into peroxisomes for conversion to mature C24 bile acids. Supporting Evidence: PMID:25168382 ABCD3 is involved in transport of branched-chain fatty acids and C27 bile acids into the peroxisome and that this is a crucial step in bile acid biosynthesis
GO:0006869 lipid transport	IEA GO_REF:0000107	ACCEPT	Summary: ABCD3 transports lipid substrates (fatty acids, bile acid intermediates) across the peroxisomal membrane. This is a correct but very general annotation. Reason: Correct but general. More specific terms (GO:0015910, GO:0015721) are also annotated and provide more precise functional description. Acceptable as a broader IEA annotation.
GO:0009410 response to xenobiotic stimulus	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: IEA transfer from rat ortholog. In rat, PMP70 expression may be upregulated by peroxisome proliferators (xenobiotics), but this is a transcriptional response, not a direct function of the ABCD3 protein itself. Reason: Transcriptional upregulation by xenobiotics reflects regulatory biology, not a direct function of the ABCD3 protein. This annotation conflates gene regulation with protein function.
GO:0015721 bile acid and bile salt transport	IEA GO_REF:0000107	ACCEPT	Summary: ABCD3 transports C27-bile acid CoA-ester intermediates (DHCA-CoA, THCA-CoA) into peroxisomes. Loss of ABCD3 leads to accumulation of these intermediates [PMID:25168382]. Cryo-EM studies confirm bile acid intermediates as ABCD3-specific substrates [PMID:39223112]. Reason: Well-supported by patient genetics, knockout mice, and structural studies. DHCA-CoA and THCA-CoA are ABCD3-specific substrates per cryo-EM data. Supporting Evidence: PMID:25168382 ABCD3 is involved in transport of branched-chain fatty acids and C27 bile acids into the peroxisome
GO:0042802 identical protein binding	IEA GO_REF:0000107	MODIFY	Summary: ABCD3 forms homodimers, demonstrated by FRET microscopy in living cells [PMID:17609205]. However, the more specific term GO:0042803 (protein homodimerization activity) is already annotated with IDA evidence. This IEA annotation is redundant and less informative. Reason: The more specific GO:0042803 (protein homodimerization activity) is already annotated with direct experimental evidence (IDA, PMID:17609205). This IEA term is less precise. Proposed replacements: protein homodimerization activity
GO:1903512 phytanic acid metabolic process	IEA GO_REF:0000107	ACCEPT	Summary: ABCD3 imports branched-chain fatty acids including pristanic acid (the alpha-oxidation product of phytanic acid) into peroxisomes. Abcd3 knockout mice accumulate phytanic acid after phytol loading [PMID:25168382]. The ABCD3-deficient patient showed reduced pristanic acid beta-oxidation [PMID:25168382]. Reason: Supported by knockout mouse and patient data showing impaired branched-chain fatty acid metabolism when ABCD3 is absent. Supporting Evidence: PMID:25168382 Abcd3-/- mice accumulated the branched chain fatty acid phytanic acid after phytol loading
GO:0005515 protein binding	IPI PMID:10551832 Homo- and heterodimerization of peroxisomal ATP-binding cass...	MODIFY	Summary: Demonstrates heterodimerization of ABCD3 (PMP70) with ABCD1 (ALDP) by yeast two-hybrid and co-immunoprecipitation [PMID:10551832]. Per curation guidelines, 'protein binding' is uninformative; a more specific term should be used. Reason: The interaction with ABCD1 is well-established but 'protein binding' is uninformative. Should be annotated with a more specific term reflecting heterodimerization. Proposed replacements: protein heterodimerization activity
GO:0005515 protein binding	IPI PMID:10704444 PEX19 binds multiple peroxisomal membrane proteins, is predo...	MODIFY	Summary: Demonstrates interaction of ABCD3 with PEX19, which is required for targeting ABCD3 to peroxisomes [PMID:10704444]. PEX19 is a cytosolic chaperone/import receptor for class I peroxisomal membrane proteins, of which ABCD3 is a client. Reason: Specific interaction with PEX19 (a peroxisomal biogenesis chaperone/import receptor) is well-characterized but 'protein binding' is uninformative. PEX19 is a distinct protein (not ABCD3 itself), so homo-/heterodimerization terms are inappropriate. ABCD3 binds PEX19 as a client of this chaperone, so a chaperone-binding term is the more informative molecular function. Proposed replacements: protein-folding chaperone binding Supporting Evidence: PMID:10704444 PEX19 binds multiple peroxisomal membrane proteins, is predominantly cytoplasmic, and is required for peroxisome membrane synthesis
GO:0005515 protein binding	IPI PMID:14709540 PEX19 is a predominantly cytosolic chaperone and import rece...	REMOVE	Summary: PEX19 acts as a cytosolic chaperone and import receptor for class 1 peroxisomal membrane proteins including ABCD3 [PMID:14709540]. Duplicates the PEX19 interaction from other entries. Reason: Uninformative 'protein binding' annotation. The PEX19 interaction is already captured by other annotations. Per curation guidelines, protein binding should be avoided.
GO:0005515 protein binding	IPI PMID:21102411 Structural basis for docking of peroxisomal membrane protein...	REMOVE	Summary: Structural basis for PEX19/PEX3 docking [PMID:21102411]. ABCD3 is one of many PEX19 cargo proteins studied. Again, 'protein binding' is uninformative. Reason: Uninformative 'protein binding' annotation. The PEX19 interaction is well-covered by other annotations. Per curation guidelines, protein binding should be avoided.
GO:0005324 long-chain fatty acid transmembrane transporter activity	IEA GO_REF:0000002	ACCEPT	Summary: InterPro-based annotation from IPR005283 (fatty acid transporter). Correct and consistent with experimental evidence from yeast complementation [PMID:24333844]. Reason: Correct IEA annotation consistent with IBA and experimental annotations for same term.
GO:0005524 ATP binding	IEA GO_REF:0000120	ACCEPT	Summary: Combined automated annotation. ATP binding is well-established for ABCD3 with IDA evidence [PMID:11248239, KM = 8.2 uM]. Reason: Consistent with experimentally validated annotations.
GO:0005777 peroxisome	IEA GO_REF:0000120	ACCEPT	Summary: Combined automated annotation for peroxisomal localization. Well-supported by extensive experimental evidence. Reason: Consistent with multiple IDA annotations for peroxisomal localization.
GO:0005778 peroxisomal membrane	IEA GO_REF:0000120	ACCEPT	Summary: Combined automated annotation for peroxisomal membrane localization. Reason: Consistent with extensive experimental evidence for peroxisomal membrane localization.
GO:0015910 long-chain fatty acid import into peroxisome	IEA GO_REF:0000002	ACCEPT	Summary: InterPro-based annotation. Consistent with IMP evidence from yeast complementation [PMID:24333844]. Reason: Consistent with experimental annotations.
GO:0016020 membrane	IEA GO_REF:0000002	ACCEPT	Summary: Generic membrane annotation from InterPro. Correct but very general; more specific peroxisomal membrane annotations exist. Reason: Correct but very general. Acceptable as a broad IEA annotation alongside more specific peroxisomal membrane annotations.
GO:0016887 ATP hydrolysis activity	IEA GO_REF:0000002	ACCEPT	Summary: InterPro-based annotation. Consistent with IDA evidence from NBF studies [PMID:11248239] and proteoliposome reconstitution [PMID:29397936]. Reason: Consistent with experimental annotations.
GO:0042626 ATPase-coupled transmembrane transporter activity	IEA GO_REF:0000002	ACCEPT	Summary: InterPro-based annotation. Consistent with IDA evidence from proteoliposome studies [PMID:29397936]. Reason: Consistent with IDA annotation for same term.
GO:0055085 transmembrane transport	IEA GO_REF:0000002	ACCEPT	Summary: Generic transmembrane transport annotation. Correct but very general. Reason: Correct but general. More specific transport process terms are also annotated.
GO:0140359 ABC-type transporter activity	IEA GO_REF:0000002	ACCEPT	Summary: InterPro-based annotation reflecting ABC transporter domain architecture. ABCD3 is indeed a member of the ABCD family of ABC transporters. Reason: Correct classification. ABCD3 belongs to the ABC transporter superfamily, ABCD family.
GO:0005777 peroxisome	IDA GO_REF:0000052	ACCEPT	Summary: HPA immunofluorescence data confirming peroxisomal localization of ABCD3. Reason: Core localization, independently validated by multiple methods.
GO:0005778 peroxisomal membrane	TAS Reactome:R-HSA-382575	ACCEPT	Summary: Reactome pathway: ABCD1-3 dimers transfer LCFAs from cytosol to peroxisomal matrix. Consistent with ABCD3 function. Reason: Consistent with established localization and function.
GO:0005778 peroxisomal membrane	TAS Reactome:R-HSA-382613	ACCEPT	Summary: Reactome pathway: PEX19 docks ABCD3 to peroxisomal membrane. Reason: Consistent with PEX19-mediated targeting of ABCD3 to peroxisomes.
GO:0005778 peroxisomal membrane	TAS Reactome:R-HSA-9603775	ACCEPT	Summary: Reactome pathway: PEX3:PEX19:class I PMP dissociates. ABCD3 is a class I PMP. Reason: Consistent with peroxisomal membrane protein import pathway.
GO:0005829 cytosol	TAS Reactome:R-HSA-382613	KEEP AS NON CORE	Summary: Reactome: PEX19 docks ABCD3 to peroxisomal membrane, implying ABCD3 transits through cytosol during biogenesis. ABCD3 is synthesized on free ribosomes and targeted posttranslationally [PMID:17761678]. Reason: ABCD3 passes through the cytosol during posttranslational targeting but its steady-state localization is peroxisomal membrane. Cytosol is a transient location during biogenesis, not the functional site.
GO:0005829 cytosol	TAS Reactome:R-HSA-9603775	KEEP AS NON CORE	Summary: Reactome: PEX3:PEX19:class I PMP complex dissociation. Transient cytosolic location during import pathway. Reason: Transient localization during biogenesis, not functional site.
GO:0005829 cytosol	TAS Reactome:R-HSA-9603784	KEEP AS NON CORE	Summary: Reactome: PEX19:class I PMP binds PEX3. Part of peroxisomal membrane protein import. Reason: Transient localization during biogenesis.
GO:0005829 cytosol	TAS Reactome:R-HSA-9603804	KEEP AS NON CORE	Summary: Reactome: PEX19 binds class I peroxisomal membrane proteins in cytosol. Reason: Transient localization during biogenesis.
GO:0005778 peroxisomal membrane	EXP PMID:10704444 PEX19 binds multiple peroxisomal membrane proteins, is predo...	ACCEPT	Summary: PEX19 binds ABCD3 and is required for its localization to peroxisomal membrane [PMID:10704444]. Subcellular fractionation and immunofluorescence confirm peroxisomal membrane localization. Reason: Core localization with direct experimental evidence from subcellular fractionation and immunofluorescence. Supporting Evidence: PMID:10704444 PEX19 binds multiple peroxisomal membrane proteins, is predominantly cytoplasmic, and is required for peroxisome membrane synthesis
GO:0005778 peroxisomal membrane	EXP PMID:16344115 Role of Pex19p in the targeting of PMP70 to peroxisome.	ACCEPT	Summary: PEX19 mediates targeting of PMP70 to peroxisomes [PMID:16344115]. Confirms peroxisomal membrane localization through PEX19 binding studies. Reason: Core localization confirmed by PEX19 interaction and targeting studies. Supporting Evidence: PMID:16344115 Role of Pex19p in the targeting of PMP70 to peroxisome
GO:0005778 peroxisomal membrane	EXP PMID:17761678 Hydrophobic regions adjacent to transmembrane domains 1 and ...	ACCEPT	Summary: Hydrophobic regions adjacent to TMDs 1 and 5 are required for PMP70 targeting to peroxisomal membrane [PMID:17761678]. Mutagenesis of targeting signals (L21Q/L22Q/L23Q, I70N/L71Q, I307A/L308A) abolishes peroxisomal localization. Reason: Core localization. Detailed targeting signal mapping confirms peroxisomal membrane as the destination. Supporting Evidence: PMID:17761678 PMP70 possesses two distinct targeting signals, and hydrophobic regions adjacent to the first TMD of each region are important for targeting
GO:0005778 peroxisomal membrane	EXP PMID:24333844 A role for the human peroxisomal half-transporter ABCD3 in t...	ACCEPT	Summary: Subcellular fractionation and functional studies in yeast confirm ABCD3 localizes to peroxisomal membrane [PMID:24333844]. Reason: Core localization confirmed in context of substrate transport studies.
GO:0005778 peroxisomal membrane	EXP PMID:29397936 Characterization of human ATP-binding cassette protein subfa...	ACCEPT	Summary: ABCD3 reconstituted into proteoliposomes for functional studies, confirming membrane protein nature [PMID:29397936]. Reason: Core localization confirmed in proteoliposome reconstitution.
GO:0052817 very long-chain fatty acyl-CoA hydrolase activity	EXP PMID:29397936 Characterization of human ATP-binding cassette protein subfa...	ACCEPT	Summary: ABCD3 reconstituted in proteoliposomes displays acyl-CoA thioesterase activity, cleaving fatty acyl-CoA into free fatty acid and CoA [PMID:29397936]. This activity is shared by ABCD1-4. Reason: Directly demonstrated in purified reconstituted system. The thioesterase activity is proposed to hydrolyze fatty acyl-CoAs prior to ATP-dependent transport. Supporting Evidence: PMID:29397936 ABCD1-4 were found to possess an equal levels of acyl-CoA thioesterase activity
GO:0005324 long-chain fatty acid transmembrane transporter activity	IMP PMID:24333844 A role for the human peroxisomal half-transporter ABCD3 in t...	ACCEPT	Summary: Expression of human ABCD3 in pxa1/pxa2-delta yeast mutants partially rescues fatty acid oxidation, demonstrating transporter function [PMID:24333844]. ABCD3 preferentially transports hydrophilic substrates including long-chain unsaturated fatty acids. Reason: Core function demonstrated by yeast complementation assay. Key evidence for substrate specificity of ABCD3. Supporting Evidence: PMID:24333844 most hydrophilic substrates like long-chain unsaturated-, long branched-chain- and long-chain dicarboxylic fatty acids by HsABCD3
GO:0006699 bile acid biosynthetic process	ISS GO_REF:0000024	ACCEPT	Summary: ISS from mouse ortholog P55096. Well-supported by ABCD3-deficient patient showing accumulation of C27-bile acid intermediates [PMID:25168382] and Abcd3 KO mice with reduced C24 bile acids and increased C27 intermediates [PMID:25168382, PMID:34564857]. Reason: Core function. ABCD3 imports bile acid CoA-ester intermediates into peroxisomes for side-chain shortening, an essential step in bile acid biosynthesis. Supporting Evidence: PMID:25168382 ABCD3 is involved in transport of branched-chain fatty acids and C27 bile acids into the peroxisome and that this is a crucial step in bile acid biosynthesis
GO:0015721 bile acid and bile salt transport	ISS GO_REF:0000024	ACCEPT	Summary: ISS from mouse ortholog. ABCD3 transports bile acid CoA-ester intermediates (DHCA-CoA, THCA-CoA) into peroxisomes. Supported by human genetics [PMID:25168382] and cryo-EM structural data showing these are ABCD3-specific substrates [PMID:39223112]. Reason: Core function. DHCA-CoA and THCA-CoA are ABCD3-specific substrates per cryo-EM data. In vivo loss-of-function confirms bile acid transport role. Supporting Evidence: PMID:25168382 both in the patient and in Abcd3-/- mice, there was evidence of a bile acid biosynthesis defect
GO:0015910 long-chain fatty acid import into peroxisome	IMP PMID:24333844 A role for the human peroxisomal half-transporter ABCD3 in t...	ACCEPT	Summary: ABCD3 expression in pxa1/pxa2-delta yeast rescues fatty acid oxidation, demonstrating import of long-chain fatty acids into peroxisomes [PMID:24333844]. Reason: Core function with direct IMP evidence. Supporting Evidence: PMID:24333844 the phenotype of the pxa1/pxa2Delta yeast mutant, i.e. impaired oxidation of oleic acid, cannot only be partially rescued by HsABCD1, HsABCD2, but also by HsABCD3
GO:1903512 phytanic acid metabolic process	ISS GO_REF:0000024	ACCEPT	Summary: ISS from mouse ortholog. ABCD3 imports pristanic acid (and by extension contributes to phytanic acid metabolism) into peroxisomes. Abcd3 KO mice accumulate phytanic acid [PMID:25168382]. Reason: Well-supported by knockout mouse data and patient studies showing reduced pristanic acid beta-oxidation. Supporting Evidence: PMID:25168382 Abcd3-/- mice accumulated the branched chain fatty acid phytanic acid after phytol loading
GO:0000038 very long-chain fatty acid metabolic process	IDA PMID:29397936 Characterization of human ATP-binding cassette protein subfa...	KEEP AS NON CORE	Summary: ABCD3 reconstituted in proteoliposomes demonstrates thioesterase and ATPase activities with fatty acyl-CoA substrates [PMID:29397936], contributing to VLCFA metabolism. Reason: ABCD3 can process VLCFAs but this is not its primary substrate preference. ABCD1 is the main VLCFA transporter. The ABCD3-deficient patient had normal C26:0 beta-oxidation [PMID:25168382], indicating ABCD3 is not essential for VLCFA catabolism. Supporting Evidence: PMID:25168382 Peroxisomal beta-oxidation of C26:0 was normal
GO:0005777 peroxisome	IDA PMID:24333844 A role for the human peroxisomal half-transporter ABCD3 in t...	ACCEPT	Summary: Subcellular fractionation confirms ABCD3 localization to peroxisomes [PMID:24333844]. Reason: Core localization.
GO:0016887 ATP hydrolysis activity	IDA PMID:11248239 Characterization and functional analysis of the nucleotide b...	ACCEPT	Summary: Purified nucleotide binding fold (NBF) of PMP70 hydrolyzes ATP (KM = 8.2 uM). ATP-specific, no GTPase activity. Mutations G478R and S572I alter ATPase activity [PMID:11248239]. Reason: Core activity. Direct biochemical demonstration with purified protein. Supporting Evidence: PMID:11248239 Both proteins act as an ATP specific binding subunit releasing ADP after ATP hydrolysis; they did not exhibit GTPase activity
GO:0016887 ATP hydrolysis activity	IDA PMID:29397936 Characterization of human ATP-binding cassette protein subfa...	ACCEPT	Summary: ABCD3 reconstituted in proteoliposomes displays stable ATPase activity inhibited by AlF3 [PMID:29397936], confirming the NBF study findings in a full-length protein context. Reason: Core activity confirmed in full-length reconstituted protein. Supporting Evidence: PMID:29397936 ABCD1-4 displayed stable ATPase activity, which was inhibited by AlF3
GO:0042626 ATPase-coupled transmembrane transporter activity	IDA PMID:29397936 Characterization of human ATP-binding cassette protein subfa...	ACCEPT	Summary: Proteoliposome reconstitution demonstrates coupled ATPase-transport activity of ABCD3 [PMID:29397936]. Cryo-EM structures capture the conformational cycle linking ATP hydrolysis to substrate translocation [PMID:39223112]. Reason: Core molecular function. Direct demonstration in reconstituted system with structural validation of the transport mechanism. Supporting Evidence: PMID:29397936 ABCD1-3 are located on peroxisomal membrane and play an important role in the transportation of various fatty acid-CoA derivatives
GO:0047617 fatty acyl-CoA hydrolase activity	IDA PMID:29397936 Characterization of human ATP-binding cassette protein subfa...	ACCEPT	Summary: ABCD3 possesses intrinsic acyl-CoA thioesterase activity demonstrated in proteoliposomes [PMID:29397936]. This activity may hydrolyze fatty acyl-CoAs to free fatty acids prior to transport, though the cryo-EM studies suggest intact CoA-esters may also be transported. Reason: Directly demonstrated enzymatic activity. The biological significance (whether thioesterase activity is required for transport or is a side activity) remains under investigation, but the activity is real. Supporting Evidence: PMID:29397936 ABCD1-4 were found to possess an equal levels of acyl-CoA thioesterase activity
GO:0006635 fatty acid beta-oxidation	IDA PMID:24333844 A role for the human peroxisomal half-transporter ABCD3 in t...	ACCEPT	Summary: ABCD3 expression in yeast mutants restores fatty acid beta-oxidation, particularly for hydrophilic substrates [PMID:24333844]. Fatty acid oxidation measurements with various substrates reveal distinctive substrate preferences. Reason: Core function supported by direct biochemical evidence. Supporting Evidence: PMID:24333844 the phenotype of the pxa1/pxa2Delta yeast mutant, i.e. impaired oxidation of oleic acid, cannot only be partially rescued by HsABCD1, HsABCD2, but also by HsABCD3
GO:0006633 fatty acid biosynthetic process	IMP PMID:25168382 A novel bile acid biosynthesis defect due to a deficiency of...	MODIFY	Summary: This annotation is problematic. PMID:25168382 describes a bile acid biosynthesis defect in an ABCD3-deficient patient, not a fatty acid biosynthesis defect. The patient showed accumulation of C27-bile acid intermediates. ABCD3 does not synthesize fatty acids; it imports them for degradation. The correct annotation should be GO:0006699 (bile acid biosynthetic process), which is already annotated separately. Reason: PMID:25168382 describes a bile acid biosynthesis defect, not fatty acid biosynthesis. ABCD3 imports substrates for beta-oxidation (catabolism), not biosynthesis. The KO mice showed altered lipogenesis [PMID:34564857] as a secondary metabolic effect, but this is not a direct function of ABCD3. The correct term for the primary finding is bile acid biosynthetic process. Proposed replacements: bile acid biosynthetic process Supporting Evidence: PMID:25168382 A novel bile acid biosynthesis defect due to a deficiency of peroxisomal ABCD3
GO:0016020 membrane	HDA PMID:19946888 Defining the membrane proteome of NK cells.	ACCEPT	Summary: High-throughput proteomics identification of ABCD3 in NK cell membrane fractions [PMID:19946888]. Generic membrane annotation. Reason: Correct but very general. ABCD3 is indeed a membrane protein. More specific peroxisomal membrane annotations provide better functional context.
GO:0005782 peroxisomal matrix	IDA PMID:9765053 Restoration of PEX2 peroxisome assembly defects by overexpre...	REMOVE	Summary: PMID:9765053 describes restoration of PEX2 peroxisome assembly defects by overexpression of PMP70. ABCD3 is a multi-pass transmembrane protein with its NBD domain extending into the cytosol. The annotation to peroxisomal matrix is problematic for a transmembrane protein, unless referring to the NBD domain facing the matrix side. However, cryo-EM structures show the NBDs are cytosolic [PMID:39223112]. Reason: ABCD3 is an integral membrane protein of the peroxisomal membrane with its NBD domain in the cytosol. It is not a peroxisomal matrix protein. The cryo-EM structures confirm the cytosolic orientation of the NBDs [PMID:39223112]. Peroxisomal matrix annotation is incorrect for this transmembrane protein.
GO:0007031 peroxisome organization	IMP PMID:9765053 Restoration of PEX2 peroxisome assembly defects by overexpre...	KEEP AS NON CORE	Summary: Overexpression of PMP70 restores peroxisome assembly in PEX2-deficient cells [PMID:9765053]. This is an indirect effect of providing abundant peroxisomal membrane protein. Reason: Not a direct function. The rescue of peroxisome assembly defects by PMP70 overexpression is an indirect compensatory effect, not evidence of a primary role in peroxisome organization. Supporting Evidence: PMID:9765053 Restoration of PEX2 peroxisome assembly defects by overexpression of PMP70
GO:0005777 peroxisome	IDA PMID:17542813 Adrenoleukodystrophy: subcellular localization and degradati...	ACCEPT	Summary: Immunofluorescence study showing ABCD3 localizes to peroxisomes [PMID:17542813]. The paper primarily studies ABCD1/ALDP but confirms ABCD3 peroxisomal localization. Reason: Core localization confirmed by immunofluorescence.
GO:0005777 peroxisome	IDA PMID:20007743 Multiple organelle-targeting signals in the N-terminal porti...	ACCEPT	Summary: Multiple targeting signals in the N-terminal portion of PMP70 direct it to peroxisomes [PMID:20007743]. Confirms peroxisomal localization. Reason: Core localization. Supporting Evidence: PMID:20007743 Cooperation of the organelle-targeting signals enables PMP70 to correctly target to peroxisomal membranes
GO:0005777 peroxisome	IDA PMID:19479899 Pex3p-dependent peroxisomal biogenesis initiates in the endo...	ACCEPT	Summary: Pex3p-dependent peroxisomal biogenesis initiates in the ER of human fibroblasts [PMID:19479899]. ABCD3 used as a peroxisomal marker. Reason: Core localization; ABCD3 is routinely used as a peroxisomal marker.
GO:0006635 fatty acid beta-oxidation	IGI PMID:9425230 Suppression of peroxisomal membrane protein defects by perox...	ACCEPT	Summary: Expression of PMP70 restores VLCFA beta-oxidation in X-ALD (ABCD1-deficient) fibroblasts, demonstrating overlapping function between ABCD1 and ABCD3 in fatty acid beta-oxidation [PMID:9425230]. Reason: Core function. IGI evidence from complementation showing ABCD3 can substitute for ABCD1 in supporting VLCFA beta-oxidation. Supporting Evidence: PMID:9425230 Expression of either ALDP or PMP70 restores VLCFA beta-oxidation in X-ALD fibroblasts, indicating overlapping functions
GO:0007031 peroxisome organization	IDA PMID:9425230 Suppression of peroxisomal membrane protein defects by perox...	KEEP AS NON CORE	Summary: ABCD3 expression restores peroxisome biogenesis in PEX2-deficient cells [PMID:9425230]. Indirect effect of providing peroxisomal membrane components. Reason: Not a direct function. Same indirect rescue as PMID:9765053. Supporting Evidence: PMID:9425230 Their expression also restores peroxisome biogenesis in cells that are deficient in the peroxisomal membrane protein Pex2p
GO:0042760 very long-chain fatty acid catabolic process	IGI PMID:9425230 Suppression of peroxisomal membrane protein defects by perox...	KEEP AS NON CORE	Summary: ABCD3 expression restores VLCFA beta-oxidation in ABCD1-deficient cells [PMID:9425230]. Reason: ABCD3 can contribute to VLCFA catabolism but it is not the primary VLCFA transporter. ABCD1 handles C24:0/C26:0 preferentially [PMID:24333844]. The ABCD3-deficient patient had normal C26:0 beta-oxidation [PMID:25168382]. Supporting Evidence: PMID:9425230 Expression of either ALDP or PMP70 restores VLCFA beta-oxidation in X-ALD fibroblasts, indicating overlapping functions
GO:0005515 protein binding	IPI PMID:10777694 Human adrenoleukodystrophy protein and related peroxisomal A...	REMOVE	Summary: Interaction of ABCD3 with PEX19 demonstrated by various binding assays [PMID:10777694]. Per curation guidelines, 'protein binding' is uninformative. Reason: Uninformative. The PEX19 interaction is functionally relevant for peroxisomal targeting but 'protein binding' does not capture this. The interaction is already reflected in the peroxisomal membrane localization annotations.
GO:0005515 protein binding	IPI PMID:17609205 Live cell FRET microscopy: homo- and heterodimerization of t...	REMOVE	Summary: FRET microscopy demonstrating ABCD3 homo- and heterodimerization with ABCD1 in living cells [PMID:17609205]. The specific homodimerization function is already annotated as GO:0042803 (protein homodimerization activity) with IDA evidence from the same paper. Reason: Uninformative. The functional interaction is better captured by GO:0042803 (protein homodimerization activity) already annotated from this same reference.
GO:0005777 peroxisome	IDA PMID:9425230 Suppression of peroxisomal membrane protein defects by perox...	ACCEPT	Summary: ABCD3 localizes to peroxisomes [PMID:9425230]. Reason: Core localization.
GO:0005778 peroxisomal membrane	IDA PMID:17609205 Live cell FRET microscopy: homo- and heterodimerization of t...	ACCEPT	Summary: FRET microscopy in living cells confirms ABCD3 localization to peroxisomal membrane where it forms homodimers [PMID:17609205]. Reason: Core localization with in vivo FRET confirmation. Supporting Evidence: PMID:17609205 ALDP and PMP70 form homodimers as well as ALDP/PMP70 heterodimers where ALDP homodimers predominate
GO:0042803 protein homodimerization activity	IDA PMID:17609205 Live cell FRET microscopy: homo- and heterodimerization of t...	ACCEPT	Summary: FRET microscopy in living cells demonstrates ABCD3 homodimerization [PMID:17609205]. Dimerization is necessary for functional transporter activity. Also supported by cryo-EM structures showing homodimeric assembly [PMID:39223112, PMID:40501884]. Reason: Core function. Half-transporter dimerization is essential for ABC transporter function. Structural studies confirm the homodimeric arrangement. Supporting Evidence: PMID:17609205 We demonstrate in vivo that ALDP and PMP70 form homodimers as well as ALDP/PMP70 heterodimers
GO:0005515 protein binding	IPI PMID:16344115 Role of Pex19p in the targeting of PMP70 to peroxisome.	REMOVE	Summary: PEX19 interaction with ABCD3 for peroxisomal targeting [PMID:16344115]. Reason: Uninformative 'protein binding'. The PEX19 interaction is already reflected in peroxisomal membrane localization annotations.
GO:0005777 peroxisome	IDA PMID:16344115 Role of Pex19p in the targeting of PMP70 to peroxisome.	ACCEPT	Summary: ABCD3 localization to peroxisomes confirmed in PEX19 targeting studies [PMID:16344115]. Reason: Core localization.
GO:0005515 protein binding	IPI PMID:11453642 Targeting elements in the amino-terminal part direct the hum...	REMOVE	Summary: Targeting elements in the N-terminal part of PMP70 [PMID:11453642]. PEX19 interaction. Reason: Uninformative 'protein binding'. PEX19 interaction covered elsewhere.
GO:0005524 ATP binding	IDA PMID:11248239 Characterization and functional analysis of the nucleotide b...	ACCEPT	Summary: Direct measurement of ATP binding by purified NBF of PMP70 with KM = 8.2 uM [PMID:11248239]. ATP-specific, no GTP binding. Reason: Core function with direct biochemical evidence. Supporting Evidence: PMID:11248239 Both proteins act as an ATP specific binding subunit releasing ADP after ATP hydrolysis
GO:0005777 peroxisome	IDA PMID:11453642 Targeting elements in the amino-terminal part direct the hum...	ACCEPT	Summary: ABCD3 localizes to peroxisomes [PMID:11453642]. Reason: Core localization.
GO:0005515 protein binding	IPI PMID:11590176 Two different targeting signals direct human peroxisomal mem...	REMOVE	Summary: Two different targeting signals direct human PMP22 to peroxisomes [PMID:11590176]. ABCD3 interaction context. Uninformative term. Reason: Uninformative 'protein binding'.
GO:0005515 protein binding	IPI PMID:11883941 Two splice variants of human PEX19 exhibit distinct function...	REMOVE	Summary: PEX19 splice variants and their functions in peroxisomal assembly [PMID:11883941]. ABCD3 as PEX19 cargo. Uninformative term. Reason: Uninformative 'protein binding'. PEX19 interaction covered by other annotations.
GO:0005777 peroxisome	IDA PMID:9922452 Peroxisome synthesis in the absence of preexisting peroxisom...	ACCEPT	Summary: Peroxisome synthesis in the absence of preexisting peroxisomes [PMID:9922452]. ABCD3 used as peroxisomal marker. Reason: Core localization.
GO:0005777 peroxisome	IDA PMID:10704444 PEX19 binds multiple peroxisomal membrane proteins, is predo...	ACCEPT	Summary: ABCD3 localizes to peroxisomes, requires PEX19 for targeting [PMID:10704444]. Reason: Core localization.
GO:0015125 bile acid transmembrane transporter activity	IMP PMID:25168382 A novel bile acid biosynthesis defect due to a deficiency of...	NEW	Summary: ABCD3 specifically transports C27-bile acid CoA-ester intermediates (DHCA-CoA, THCA-CoA) across the peroxisomal membrane. Loss of ABCD3 causes accumulation of these intermediates in patient plasma [PMID:25168382] and in Abcd3 KO mice [PMID:25168382, PMID:34564857]. Cryo-EM structural data identifies these bile acid intermediates as ABCD3-specific substrates [PMID:39223112]. The existing annotations capture the bile acid transport process (GO:0015721) but no molecular function term for bile acid transporter activity is present. Reason: ABCD3 catalyzes transmembrane transport of bile acid CoA-esters across the peroxisomal membrane. The existing process annotation GO:0015721 (bile acid and bile salt transport) covers the broader biological process. This molecular function term captures the direct transporter activity and is supported by patient genetics, KO mice, and cryo-EM substrate-binding data. Supporting Evidence: PMID:25168382 ABCD3 is involved in transport of branched-chain fatty acids and C27 bile acids into the peroxisome
GO:0046982 protein heterodimerization activity	IDA PMID:17609205 Live cell FRET microscopy: homo- and heterodimerization of t...	NEW	Summary: ABCD3 forms heterodimers with ABCD1 and ABCD2, demonstrated by FRET microscopy in living cells [PMID:17609205] and by yeast two-hybrid and co-immunoprecipitation [PMID:10551832]. This is a more informative annotation than the generic 'protein binding' currently annotated for the ABCD1/ABCD3 interaction. Reason: Replaces uninformative 'protein binding' annotations. ABCD3 heterodimerization with ABCD1 is well-established and functionally relevant, as it creates transporters with potentially different substrate preferences. Supporting Evidence: PMID:17609205 We demonstrate in vivo that ALDP and PMP70 form homodimers as well as ALDP/PMP70 heterodimers PMID:10551832 Co-immunoprecipitation demonstrated the homodimerization of ALDP, the heterodimerization of ALDP with PMP70

Core Functions

ABCD3 is a peroxisomal ABC half-transporter that homodimerizes to form an active ATP-dependent transporter. It catalyzes ATP-driven import of fatty acid substrates (as CoA esters) from the cytosol into the peroxisomal lumen. Cryo-EM structures reveal an alternating-access mechanism: substrate binding to the inward-open state promotes NBD dimerization, ATP binding drives transition to outward-open state for substrate release, and ATP hydrolysis resets the transporter [PMID:39223112, PMID:40501884].

Molecular Function:

ATPase-coupled transmembrane transporter activity

Directly Involved In:

long-chain fatty acid import into peroxisome fatty acid beta-oxidation

Cellular Locations:

peroxisomal membrane

Supporting Evidence:

PMID:29397936
ABCD1-4 displayed stable ATPase activity, which was inhibited by AlF3
PMID:39223112
Upon ATP binding, ABCD3 exhibits a conformation that is open towards the peroxisomal matrix, leaving two extra densities corresponding to two CoA molecules deeply embedded in the translocation cavity
PMID:40501884
Structural comparison of the apo and substrate bound states demonstrate that the substrate interaction brings nucleotide-binding domains closer, providing a mechanistic basis of substrate induced ATPase activity

ABCD3 has broad substrate specificity among the peroxisomal ABC transporters, preferentially importing hydrophilic fatty acid substrates including long-chain unsaturated fatty acids, branched-chain fatty acids (pristanic acid), dicarboxylic acids (C14-C18), and bile acid CoA-ester intermediates (DHCA-CoA, THCA-CoA). This contrasts with ABCD1 which preferentially transports the most hydrophobic VLCFAs [PMID:24333844].

Molecular Function:

long-chain fatty acid transmembrane transporter activity

Directly Involved In:

long-chain fatty acid import into peroxisome phytanic acid metabolic process

Cellular Locations:

peroxisomal membrane

Supporting Evidence:

PMID:24333844
most hydrophilic substrates like long-chain unsaturated-, long branched-chain- and long-chain dicarboxylic fatty acids by HsABCD3

ABCD3 is the peroxisomal transporter responsible for import of C27-bile acid CoA-ester intermediates (DHCA-CoA, THCA-CoA) for side-chain shortening to mature C24 bile acids. Loss of ABCD3 causes CBAS5 with accumulation of bile acid intermediates. Structural studies identify these as ABCD3-specific substrates [PMID:25168382, PMID:39223112]. This represents a unique and non-redundant function of ABCD3 within the ABCD transporter family.

Molecular Function:

ATPase-coupled transmembrane transporter activity

Directly Involved In:

bile acid and bile salt transport bile acid biosynthetic process

Cellular Locations:

peroxisomal membrane

Supporting Evidence:

PMID:25168382
ABCD3 is involved in transport of branched-chain fatty acids and C27 bile acids into the peroxisome and that this is a crucial step in bile acid biosynthesis

ABCD3 possesses intrinsic thioesterase activity that cleaves fatty acyl-CoAs into free fatty acids and CoA. This may be mechanistically coupled to the transport process, with CoA hydrolysis occurring during or after substrate translocation [PMID:29397936]. The cryo-EM studies suggest substrates may be released either intact or after hydrolysis [PMID:40501884].

Molecular Function:

fatty acyl-CoA hydrolase activity

Cellular Locations:

peroxisomal membrane

Supporting Evidence:

PMID:29397936
ABCD1-4 were found to possess an equal levels of acyl-CoA thioesterase activity

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000024

Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000052

Gene Ontology annotation based on curation of immunofluorescence data

GO_REF:0000107

Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:9425230

Suppression of peroxisomal membrane protein defects by peroxisomal ATP binding cassette (ABC) proteins.

Expression of PMP70 restores VLCFA beta-oxidation in X-ALD fibroblasts
PMP70 and ALDP expression restores peroxisome biogenesis in PEX2-deficient cells
Indicates overlapping functions between peroxisomal ABC transporters

PMID:9765053

Restoration of PEX2 peroxisome assembly defects by overexpression of PMP70.

PMP70 overexpression rescues PEX2-deficient peroxisome assembly

PMID:9922452

Peroxisome synthesis in the absence of preexisting peroxisomes.

ABCD3 used as peroxisomal marker to track de novo peroxisome synthesis

PMID:10551832

Homo- and heterodimerization of peroxisomal ATP-binding cassette half-transporters.

ABCD3 (PMP70) homo- and heterodimerizes with ABCD1 (ALDP) and ABCD2 (ALDRP)
Demonstrated by yeast two-hybrid and co-immunoprecipitation
C-terminal halves mediate dimerization

PMID:10704444

PEX19 binds multiple peroxisomal membrane proteins, is predominantly cytoplasmic, and is required for peroxisome membrane synthesis.

PEX19 binds ABCD3 and is required for peroxisomal membrane targeting
PEX19 is predominantly cytoplasmic

PMID:10777694

Human adrenoleukodystrophy protein and related peroxisomal ABC transporters interact with the peroxisomal assembly protein PEX19p.

ABCD3 interacts with PEX19 for peroxisomal targeting

PMID:11248239

Characterization and functional analysis of the nucleotide binding fold in human peroxisomal ATP binding cassette transporters.

PMP70 NBF binds ATP with KM of 8.2 uM
ATP-specific, no GTPase activity
G478R mutation decreases ATP binding; S572I decreases ATPase activity
NBF mutations do not affect dimerization

PMID:11453642

Targeting elements in the amino-terminal part direct the human 70-kDa peroxisomal integral membrane protein (PMP70) to peroxisomes.

N-terminal targeting elements required for peroxisomal localization

PMID:11590176

Two different targeting signals direct human peroxisomal membrane protein 22 to peroxisomes.

PMID:11883941

Two splice variants of human PEX19 exhibit distinct functions in peroxisomal assembly.

PMID:14709540

PEX19 is a predominantly cytosolic chaperone and import receptor for class 1 peroxisomal membrane proteins.

ABCD3 is a class 1 PMP that uses PEX19 as chaperone/import receptor

PMID:16344115

Role of Pex19p in the targeting of PMP70 to peroxisome.

PEX19 N-terminal region interacts with ABCD3 N-terminus (aa 1-61)
Required for peroxisomal targeting

PMID:17542813

Adrenoleukodystrophy: subcellular localization and degradation of adrenoleukodystrophy protein (ALDP/ABCD1) with naturally occurring missense mutations.

ABCD3 (PMP70) used as peroxisomal marker; confirmed peroxisomal localization

PMID:17609205

Live cell FRET microscopy: homo- and heterodimerization of two human peroxisomal ABC transporters, the adrenoleukodystrophy protein (ALDP, ABCD1) and PMP70 (ABCD3).

ABCD3 forms homodimers in living cells (FRET microscopy)
Also forms ABCD1/ABCD3 heterodimers, but ABCD1 homodimers predominate
C-terminal 87 amino acids harbor the key dimerization domain

PMID:17761678

Hydrophobic regions adjacent to transmembrane domains 1 and 5 are important for the targeting of the 70-kDa peroxisomal membrane protein.

PMP70 has two distinct peroxisomal targeting signals
Hydrophobic regions adjacent to TMD1 and TMD5 are critical
L21Q/L22Q/L23Q, I70N/L71Q, I307A/L308A mutations abolish targeting

PMID:19479899

Pex3p-dependent peroxisomal biogenesis initiates in the endoplasmic reticulum of human fibroblasts.

ABCD3 used as peroxisomal membrane marker

PMID:19946888

Defining the membrane proteome of NK cells.

ABCD3 identified in NK cell membrane proteome

PMID:20007743

Multiple organelle-targeting signals in the N-terminal portion of peroxisomal membrane protein PMP70.

N-terminal 80aa segment alone targets to outer mitochondrial membrane
TM1 segment alone targets to ER
Full N80-TM1-TM2 region targets exclusively to peroxisomes
N80 segment suppresses ER-targeting function of TM1

PMID:21102411

Structural basis for docking of peroxisomal membrane protein carrier Pex19p onto its receptor Pex3p.

PEX19/PEX3 docking structure relevant to ABCD3 import pathway

PMID:24333844

A role for the human peroxisomal half-transporter ABCD3 in the oxidation of dicarboxylic acids.

Each peroxisomal half-transporter can function as homodimer
ABCD3 preferentially transports hydrophilic substrates including long-chain unsaturated, branched-chain, and dicarboxylic fatty acids
Substrate specificities of ABCD1, ABCD2, and ABCD3 are overlapping but distinct
All substrates transported as CoA esters
ABCD3 has a specific role in dicarboxylic acid oxidation

PMID:25168382

A novel bile acid biosynthesis defect due to a deficiency of peroxisomal ABCD3.

First ABCD3-deficient patient identified with CBAS5
Accumulation of C27-bile acid intermediates in plasma
Normal C26:0 beta-oxidation but reduced pristanic acid beta-oxidation
Abcd3 KO mice accumulate phytanic acid and C27-bile acid intermediates
ABCD3 transports branched-chain fatty acids and C27 bile acids into peroxisomes
Critical step in bile acid biosynthesis

PMID:29397936

Characterization of human ATP-binding cassette protein subfamily D reconstituted into proteoliposomes.

ABCD3 displays stable ATPase activity inhibited by AlF3
ABCD3 possesses acyl-CoA thioesterase activity equal to ABCD1/2/4
Reconstituted in proteoliposomes for functional characterization

PMID:34564857

The peroxisomal transporter ABCD3 plays a major role in hepatic dicarboxylic fatty acid metabolism and lipid homeostasis.

Abcd3 KO mice show increased hepatic long-chain DCAs (C14-C18)
Elevated urinary medium-chain DCAs
Hepatomegaly, lipodystrophic phenotype
Elevated C27 bile acid precursors DHCA and THCA
Deficient ketone body production during fasting
Enhanced cholesterol synthesis with decreased de novo lipogenesis

PMID:39223112

Structural insights into human ABCD3-mediated peroxisomal acyl-CoA translocation.

Cryo-EM structures of ABCD3 bound to phytanoyl-CoA (2.9 A) and ATP (3.2 A)
Inward-facing and outward-facing conformational states captured
Two phytanoyl-CoA molecules bind individually to each TMD
DHCA-CoA and THCA-CoA are ABCD3-specific substrates
ATP binding causes scissor-like movement expanding translocation cavity
PDB codes 8Z0F and 8Z9X

PMID:40501884

Molecular mechanism of substrate transport by human peroxisomal ABCD3.

Cryo-EM structures of full-length ABCD3 apo (3.33 A) and phytanoyl-CoA-bound (3.13 A)
Both inward-facing conformations as homodimer
Substrate binding induces 5-fold increase in ATPase activity
Substrate binding reduces NBD separation from 38.18 to 34.28 A
Proposed transport cycle with substrate-induced NBD closure

Reactome:R-HSA-382575

ABCD1-3 dimers transfer LCFAs from cytosol to peroxisomal matrix

Reactome:R-HSA-382613

PEX-19 docks ABCD1/D2/D3 to peroximal membrane

Reactome:R-HSA-9603775

PEX3:PEX19:class I PMP dissociates

Reactome:R-HSA-9603784

PEX19:class I PMP binds PEX3

Reactome:R-HSA-9603804

PEX19 binds class I peroxisomal membrane proteins

Suggested Experiments

Experiment: In vitro reconstituted transport assays using ABCD3 proteoliposomes with radiolabeled bile acid CoA-esters (DHCA-CoA, THCA-CoA) to directly demonstrate ATP-dependent transport of these specific substrates and determine whether they are transported intact or hydrolyzed during translocation.

Experiment: Cryo-EM structures of ABCD3 bound to bile acid CoA-ester substrates to complement the existing phytanoyl-CoA-bound structures and reveal any substrate-specific binding modes.

Experiment: Functional characterization of ABCD3/ABCD1 and ABCD3/ABCD2 heterodimers reconstituted in proteoliposomes to determine substrate specificity and transport rates compared to homodimers.

Deep Research

Falcon

(ABCD3-deep-research-falcon.md)

this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 45 citations 2026-04-23T08:14:23.424105

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Functional Annotation of Human ABCD3 / PMP70 (UniProt P28288)

0) Target verification (critical disambiguation)

The literature synthesized below consistently refers to human ABCD3, also known as PMP70 (70 kDa peroxisomal membrane protein), a peroxisomal ATP-binding cassette (ABC) subfamily D half-transporter localized to the peroxisomal membrane. Reviews describe the expected ABCD-family architecture: an N-terminal multi-pass transmembrane domain (TMD; ~6 helices) and a C-terminal cytosolic nucleotide-binding domain (NBD) with Walker A/B and ABC signature motifs, matching the UniProt P28288 description (morita2012peroxisomalabctransporters pages 2-3, tawbeh2021peroxisomalabctransporters pages 3-4, andreoletti2017predictivestructureand pages 3-5).

1) Key concepts and definitions (current understanding)

1.1 Peroxisomal ABCD transporters and “half-transporter” definition

ABCD1/ABCD2/ABCD3 are peroxisomal ABC half-transporters: each monomer contains one TMD and one NBD, and must oligomerize to form an active transporter unit (tawbeh2021peroxisomalabctransporters pages 1-3). Evidence from multiple approaches supports homo- and hetero-associations, but in vivo interactions appear predominantly homomeric, and higher-order assemblies (notably tetramers) are frequently observed for peroxisomal ABCDs (tawbeh2021peroxisomalabctransporters pages 3-4, geillon2017peroxisomalatpbindingcassette pages 11-12).

1.2 What ABCD3 does (core definition)

ABCD3’s primary role is to translocate specific lipid acyl-CoA esters from the cytosolic side into the peroxisomal lumen/matrix side, enabling peroxisomal fatty-acid oxidation and related pathways. ABCD3 is especially implicated in transport of branched-chain fatty acyl-CoAs (e.g., phytanoyl-CoA-related substrates), long-chain dicarboxylic fatty acyl-CoAs, and C27 bile-acid intermediates (DHCA/THCA CoA-esters) (li2024structuralinsightsinto pages 1-2, chornyi2021peroxisomalmetaboliteand pages 4-6).

1.3 Mechanistic uncertainty: hydrolysis during transport

A recurring concept in the field is whether peroxisomal ABCD transporters import intact acyl-CoA or whether the acyl-CoA thioester bond is hydrolyzed during/around transport with subsequent intraperoxisomal re-esterification by acyl-CoA synthetases. Reviews describe this as an active area with incomplete resolution, underscoring mechanistic complexity beyond a simple “CoA ester goes in unchanged” model (chornyi2021peroxisomalmetaboliteand pages 4-6).

2) Molecular function: substrates, ATPase activity, and transport mechanism

2.1 Best-supported transported substrates (substrate specificity)

Across reviews and experimental models, the most consistently supported ABCD3 substrate classes are:
- Branched-chain fatty acyl-CoAs (notably phytanoyl-CoA binding/transport specialization) (li2024structuralinsightsinto pages 1-2, chornyi2021peroxisomalmetaboliteand pages 4-6).
- Long-chain dicarboxylic fatty acyl-CoAs (DCAs), supporting peroxisomal ω-oxidation product metabolism (ranea‐robles2021theperoxisomaltransporter pages 1-3, ranea‐robles2021theperoxisomaltransporter pages 11-13, chornyi2021peroxisomalmetaboliteand pages 4-6).
- C27 bile-acid intermediates (CoA-esters of DHCA and THCA) required for peroxisomal side-chain shortening to mature C24 bile acids (chornyi2021peroxisomalmetaboliteand pages 4-6, li2024structuralinsightsinto pages 1-2).

ABCD3 is also described as having broad/overlapping activity with other ABCD family transporters for long- and very-long-chain fatty acyl-CoAs, but with distinct preferences (tawbeh2021peroxisomalabctransporters pages 3-4, chornyi2021peroxisomalmetaboliteand pages 4-6).

2.2 2024 structural breakthrough (cryo-EM with substrate)

A key recent advance is the cryo-EM structural characterization of human ABCD3 bound to phytanoyl-CoA and ATP (Li et al., Cell Discovery, Sep 2024, https://doi.org/10.1038/s41421-024-00722-8). The structures show two phytanoyl-CoA molecules bound and conformational states consistent with an ATP-driven transport cycle, providing direct structural support for substrate recognition and mechanistic transport steps (li2024structuralinsightsinto pages 1-2).

A schematic of the proposed ABCD3 transport cycle states from this study is available as a retrieved figure panel (li2024structuralinsightsinto media 7540f9ec).

2.3 Quantitative enzymology (ATPase kinetics)

Li et al. report substrate-stimulated ATPase activity with quantitative parameters for human ABCD3: Km ≈ 0.24 mM and Vmax ≈ 288.1 nmol Pi/min/mg protein, and a loss-of-function variant (E596Q) with substantially reduced Vmax ≈ 107.3 nmol Pi/min/mg; phytanoyl-CoA stimulation was highly significant (P = 0.0000436) (li2024structuralinsightsinto pages 1-2). These values provide concrete biochemical support that ABCD3 is an ATP-powered transporter responsive to a branched-chain acyl-CoA substrate.

3) Biological processes and pathways involving ABCD3

3.1 Peroxisomal β-oxidation and metabolic crosstalk

ABCD3 supports peroxisomal β-oxidation by enabling entry of appropriate lipid substrates. In Abcd3 knockout mouse models, metabolic phenotypes are consistent with impaired peroxisomal handling of DCAs and compensatory mitochondrial metabolism, reinforcing a peroxisome–mitochondria division of labor (ranea‐robles2021theperoxisomaltransporter pages 10-11).

3.2 Dicarboxylic fatty acid (DCA) metabolism (ω-oxidation products)

A central in vivo role for ABCD3 is in hepatic DCA metabolism. In Abcd3 knockout mice, investigators report increased hepatic long-chain DCAs and marked medium-chain dicarboxylic aciduria, particularly C8-DCA, together with broader lipid homeostasis changes (lipodystrophy; cholesterol synthesis changes) (Ranea-Robles et al., J Inherited Metabolic Disease, Oct 2021, https://doi.org/10.1002/jimd.12440) (ranea‐robles2021theperoxisomaltransporter pages 11-13).

Precision-cut liver slice experiments further support mitochondrial compensation: inhibition of mitochondrial FAO modulated medium-chain DCA accumulation, consistent with DCAs being rerouted toward mitochondria when peroxisomal import is impaired (ranea‐robles2021theperoxisomaltransporter pages 10-11).

3.3 Bile-acid biosynthesis (C27-to-C24 side-chain shortening)

Multiple sources converge that ABCD3 transports CoA-esters of C27 bile-acid intermediates (DHCA/THCA) into peroxisomes for subsequent side-chain shortening by β-oxidation enzymes. Human deficiency and mouse knockout models show accumulation of these intermediates (chornyi2021peroxisomalmetaboliteand pages 4-6, imanaka2019biogenesisandfunction pages 8-9).

3.4 Ether lipid / plasmalogen synthesis (2023 mechanistic link)

A 2023 study connects peroxisomal ABCD transporters (including ABCD3) to provision of long-chain acyl-CoAs needed for early steps of de novo ether phospholipid (plasmalogen) synthesis (Chornyi et al., Journal of Lipid Research, May 2023, https://doi.org/10.1016/j.jlr.2023.100364). The study emphasizes ABCD3 as the predominant peroxisomal ABCD transporter importing long-chain acyl-CoA esters in HeLa cells, and reports that combined disruption of ABCD1 and ABCD3 can depress ether lipid synthesis to levels similar to peroxisome-deficient cells, supporting an ABCD-dependent import requirement for this pathway context (chornyi2023theoriginof pages 6-7, chornyi2023theoriginof pages 1-2).

4) Subcellular localization, topology, oligomerization, and interaction partners

4.1 Localization and topology

ABCD3 is a peroxisomal membrane protein (tawbeh2021peroxisomalabctransporters pages 3-4). Classical topology models of peroxisomal ABCD proteins describe an N-terminal TMD and a C-terminal NBD exposed to the cytosol; protease experiments support cytosolic exposure of the NBD for ABCD3 family members (morita2012peroxisomalabctransporters pages 2-3, kemp2011mammalianperoxisomalabc pages 8-9). Topology predictions generally support six TMs, but detailed TM boundaries (especially TMH3/TMH6) have historically shown prediction variability across tools (andreoletti2017predictivestructureand pages 3-5).

4.2 Oligomeric state: dimers within tetrameric assemblies

Reviews summarize that ABCD proteins must dimerize for activity and are thought to exist mainly as tetramers in membranes (tawbeh2021peroxisomalabctransporters pages 1-3). Experimental work supports both homo- and hetero-associations; however, mammalian liver studies have suggested homomeric interactions prevail for ALDP (ABCD1) and PMP70 (ABCD3) (geillon2017peroxisomalatpbindingcassette pages 11-12, tawbeh2021peroxisomalabctransporters pages 3-4).

4.3 Targeting/biogenesis determinants and peroxisome insertion machinery

Mechanistic reviews highlight ABCD3 peroxisome targeting signals distributed in the N-terminus and other regions; ABCD3 insertion into peroxisomal membranes depends on the peroxisomal membrane protein chaperone/receptor PEX19 and docking factor PEX3 (morita2012peroxisomalabctransporters pages 3-4, tawbeh2021peroxisomalabctransporters pages 10-11). ABCD3 biogenesis also involves chaperone interactions that help it avoid mistargeting through the SRP/ER route (imanaka2019biogenesisandfunction pages 8-9).

4.4 Interaction partners (functional context)

Reported interaction/association partners provide mechanistic plausibility for substrate channeling:
- ACSL1 (ER acyl-CoA synthetase) co-immunoprecipitation/interaction evidence with ABCD3, consistent with supplying activated substrates for peroxisomal oxidation (tawbeh2021peroxisomalabctransporters pages 11-13).
- ACBD5, proposed to present VLCFA-CoA substrates to ABCD proteins, also interacts with ACSL1, supporting a substrate-transfer/contact-site model involving ABCD3 (tawbeh2021peroxisomalabctransporters pages 11-13).
- PHYH (phytanoyl-CoA 2-hydroxylase) appears in ABCD3 interactome mapping, consistent with importing phytanoyl-CoA for peroxisomal α-oxidation where PHYH catalyzes the first step (tawbeh2021peroxisomalabctransporters pages 11-13).

5) Regulation (expression control and modulation)

Evidence indicates ABCD3 can be induced by lipid-modulating agents and nuclear receptor signaling:
- A review reports ABCD3/PMP70 is inducible by fibrates (e.g., ciprofibrate, fenofibrate) via PPARα (imanaka2019biogenesisandfunction pages 9-10).
- Another authoritative review summarizes strong induction of PMP70 by PPARα ligands in rodents (e.g., ~10-fold in some mouse tissues with fenofibrate) and notes uncertainty in human promoter elements (lack of an apparent PPRE reported for the human gene in that review), emphasizing species/regulatory differences and knowledge gaps (kemp2011mammalianperoxisomalabc pages 8-9).

Direct evidence for specific ABCD3 post-translational modifications (e.g., phosphorylation) was not captured in the retrieved evidence excerpts; reviews note such topics exist in the broader literature but were not directly extractable here (tawbeh2021peroxisomalabctransporters pages 14-16).

6) Disease associations and real-world implementations

6.1 Mendelian disease: Congenital bile acid synthesis defect 5 (CBAS5) / ABCD3 deficiency

The most direct causal disease association is ABCD3 deficiency (often termed CBAS5), characterized by defective peroxisomal import of bile-acid intermediates and associated liver disease.

A 2025 clinical review (Clayton et al., J Inherited Metabolic Disease, Aug 2025, https://doi.org/10.1002/jimd.70081) describes the index patient: hepatosplenomegaly and severe progressive liver dysfunction with very high plasma DHCA and THCA, ultimately requiring liver transplantation at age 4 (clayton2025treatmentofinborn pages 11-12). Earlier mechanistic/animal work aligns with this biochemical signature: Abcd3 KO mice accumulate C27 bile-acid precursors and show hepatic disease features (ranea‐robles2021theperoxisomaltransporter pages 11-13).

A notable diagnostic point raised in the Abcd3 KO study is that C27 bile acid precursors are not routinely measured clinically, which may contribute to underdiagnosis; medium-chain DCA elevations are also relatively nonspecific, though long-chain DCA patterns may be more informative if validated in plasma (ranea‐robles2021theperoxisomaltransporter pages 11-13).

6.2 Cancer/prognosis associations (expression-based, not causal loss-of-function)

Recent cancer genomics work has evaluated ABCD3 expression as a prognostic biomarker. A 2025 study in clear cell renal cell carcinoma reports discrimination and survival metrics for ABCD3: AUC = 0.613 (p < 0.0001) and Cox regression suggesting ABCD3 expression is associated with improved survival (univariate HR 0.5435, multivariate HR 0.4534) (Heyliger et al., Cancer Genomics & Proteomics, Aug 2025, https://doi.org/10.21873/cgp.20530) (heyliger2025analysisofperoxisomal pages 7-10). These are association studies and should not be interpreted as demonstrating that ABCD3 is a driver of cancer phenotypes.

7) Recent developments (prioritizing 2023–2024)

2023 (ether lipid/plasmalogen synthesis): ABCD3 is highlighted as a predominant importer of long-chain acyl-CoAs supporting peroxisome-dependent steps in ether lipid synthesis, linking ABC transporter activity and β-oxidation-derived chain-shortened products to plasmalogen biogenesis (Chornyi et al., May 2023) (chornyi2023theoriginof pages 6-7, chornyi2023theoriginof pages 1-2).
2024 (ABCD3 cryo-EM structures): Direct visualization of phytanoyl-CoA binding and ATP-driven conformational states provides the strongest current mechanistic evidence for ABCD3’s substrate recognition and transport cycle; the paper also provides quantitative ATPase kinetics for functional interpretation and variant impact (Li et al., Sep 2024) (li2024structuralinsightsinto pages 1-2, li2024structuralinsightsinto media 7540f9ec).

8) Current applications and implementations

Clinical metabolite profiling for suspected peroxisomal/bile-acid synthesis disorders: DHCA/THCA and related C27 bile-acid intermediate patterns are central biochemical signatures of peroxisomal steps in bile-acid synthesis and are specifically implicated in ABCD3 deficiency (clayton2025treatmentofinborn pages 11-12, tawbeh2021peroxisomalabctransporters pages 3-4).
Model systems for mechanism and diagnostic marker development: Abcd3 KO mice provide an experimentally tractable system showing DCA accumulation and bile-acid intermediate changes, proposed as useful for understanding ABCD3 deficiency pathophysiology and improving diagnostic approaches (ranea‐robles2021theperoxisomaltransporter pages 13-15).
Variant interpretation / mechanistic inference: 2024 structural data can inform how specific variants could impair substrate binding or ATPase coupling, though ABCD3-targeted therapies are not established (li2024structuralinsightsinto pages 1-2).

9) Statistics and quantitative data (from recent and authoritative studies)

Transporter enzymology: ABCD3 ATPase Km ~0.24 mM, Vmax ~288.1 nmol Pi/min/mg; E596Q variant Vmax ~107.3 nmol Pi/min/mg; phytanoyl-CoA stimulation P = 0.0000436 (Li et al., 2024) (li2024structuralinsightsinto pages 1-2).
Cell functional assay: ABCD3 overexpression increased palmitate β-oxidation by about 2-fold in CHO-cell experiments summarized in a review of peroxisomal metabolite transport (chornyi2021peroxisomalmetaboliteand pages 4-6).
Ether lipid context statistic: plasmalogens constitute about ~18% of human phospholipids (Chornyi et al., 2023) (chornyi2023theoriginof pages 1-2).
Cancer prognostic association: ccRCC ABCD3 biomarker performance AUC 0.613 (p<0.0001) and Cox HRs (univariate 0.5435, multivariate 0.4534) (Heyliger et al., 2025) (heyliger2025analysisofperoxisomal pages 7-10).

10) Evidence-grounded synthesis (expert-style interpretation)

Taken together, the strongest evidence supports ABCD3 as a peroxisomal acyl-CoA transporter specialized for branched-chain substrates (e.g., phytanoyl-CoA), dicarboxylic fatty acyl-CoAs, and C27 bile-acid intermediates, with ATP-driven conformational cycling directly visualized by cryo-EM in 2024 and supported by quantitative substrate-stimulated ATPase measurements (li2024structuralinsightsinto pages 1-2, li2024structuralinsightsinto media 7540f9ec). In vivo knockout phenotypes connect this transport activity to hepatic DCA homeostasis and bile-acid maturation, with clinically relevant failure states culminating in severe liver disease in the reported ABCD3-deficient patient (ranea‐robles2021theperoxisomaltransporter pages 11-13, clayton2025treatmentofinborn pages 11-12). Newer 2023 work broadens ABCD3’s functional footprint by demonstrating that ABCD3-mediated import and peroxisomal β-oxidation can contribute substrates for ether lipid (plasmalogen) synthesis, potentially explaining tissue-specific vulnerability and metabolic phenotypes when peroxisomal transport is impaired (chornyi2023theoriginof pages 6-7, chornyi2023theoriginof pages 11-12).

Aspect	Summary
Identity / domains	Human ABCD3 encodes ATP-binding cassette sub-family D member 3, also called PMP70; it is a peroxisomal ABCD half-transporter with an N-terminal transmembrane region (~6 TM helices) and a C-terminal nucleotide-binding domain (NBD) containing canonical Walker A/B and ABC-signature motifs; the NBD is exposed to the cytosol. This matches UniProt P28288 and ABCD-family annotations (morita2012peroxisomalabctransporters pages 2-3, tawbeh2021peroxisomalabctransporters pages 3-4, andreoletti2017predictivestructureand pages 3-5).
Localization / topology / oligomerization	ABCD3 localizes to the peroxisomal membrane. As a half-transporter it must oligomerize; reviews and biochemical studies support homodimers and heterodimers, while native-PAGE/biochemical evidence indicates peroxisomal ABC transporters exist mainly as tetramers or higher-order assemblies, with homomeric interactions prevailing in vivo for ABCD proteins. Topology predictions favor 6 TM helices, though older annotation sources showed some uncertainty in TM boundaries (andreoletti2017predictivestructureand pages 1-3, tawbeh2021peroxisomalabctransporters pages 3-4, tawbeh2021peroxisomalabctransporters pages 1-3, geillon2017peroxisomalatpbindingcassette pages 11-12).
Substrates transported	Best-supported ABCD3 substrates are acyl-CoA esters of branched-chain fatty acids (including phytanoyl-CoA / pristanic-related substrates), long-chain dicarboxylic fatty acids, and C27 bile-acid intermediates (DHCA/THCA CoA esters). ABCD3 also shows broader overlap with other ABCD transporters for long- and very-long-chain fatty acids and can support import of long-chain acyl-CoAs used in ether-lipid synthesis (li2024structuralinsightsinto pages 1-2, tawbeh2021peroxisomalabctransporters pages 3-4, imanaka2019biogenesisandfunction pages 8-9, chornyi2023theoriginof pages 6-7, chornyi2021peroxisomalmetaboliteand pages 4-6).
Pathways	ABCD3 functions in peroxisomal β-oxidation, especially of branched-chain fatty acids, dicarboxylic fatty acids (DCAs), and bile-acid side-chain shortening. It also contributes to the supply of long-chain acyl-CoAs for ether phospholipid / plasmalogen synthesis and can participate in oxidation of medium/long-chain fatty acids when mitochondrial FAO is impaired or overloaded, illustrating peroxisome–mitochondria metabolic crosstalk (ranea‐robles2021theperoxisomaltransporter pages 1-3, ranea‐robles2021theperoxisomaltransporter pages 11-13, chornyi2023theoriginof pages 11-12, chornyi2023theoriginof pages 1-2, chornyi2021peroxisomalmetaboliteand pages 4-6).
Key experimental evidence & model	Cryo-EM (2024) resolved human ABCD3 bound to phytanoyl-CoA and ATP, directly visualizing substrate binding and transport-cycle states. Human cell studies showed ABCD3 overexpression increases palmitate β-oxidation, while ATP-binding mutants impair activity. CRISPR Abcd3 knockout mice and liver-slice tracer studies demonstrated defective DCA metabolism, altered bile-acid intermediates, and compensation by mitochondrial FAO. Prior human deficiency data linked ABCD3 loss to abnormal bile-acid intermediates and severe liver disease (li2024structuralinsightsinto pages 1-2, ranea‐robles2021theperoxisomaltransporter pages 11-13, ranea‐robles2021theperoxisomaltransporter pages 10-11, chornyi2021peroxisomalmetaboliteand pages 4-6, li2024structuralinsightsinto media 7540f9ec).
Disease associations / phenotypes	The clearest Mendelian disease link is congenital bile acid synthesis defect type 5 (CBAS5) / ABCD3 deficiency, associated with severe liver disease, hepatosplenomegaly, and accumulation of C27 bile-acid intermediates (DHCA/THCA). Mouse models additionally show lipodystrophy, hepatomegaly/cholestasis, altered hepatic lipid homeostasis, and increased reliance on mitochondrial DCA oxidation; reviews also note relevance to broader peroxisomal disease diagnostics and possible cancer-associated metabolic remodeling, though these are less directly causal than CBAS5 (li2024structuralinsightsinto pages 1-2, tawbeh2021peroxisomalabctransporters pages 3-4, ranea‐robles2021theperoxisomaltransporter pages 11-13).
Recent 2023–2024 developments	2023: work on ether-lipid synthesis established that ABCD3 is a major importer of long-chain acyl-CoAs supporting de novo plasmalogen synthesis and that peroxisomal β-oxidation can generate C16/C18 acyl chains for this pathway. 2024: the first ABCD3 cryo-EM structures provided direct structural insight into phytanoyl-CoA recognition, ATP-driven conformational change, and mechanistic differences from ABCD1, strengthening the conclusion that ABCD3 is specialized for branched-chain / bile-acid / DCA-related acyl-CoAs (li2024structuralinsightsinto pages 1-2, chornyi2023theoriginof pages 11-12, chornyi2023theoriginof pages 6-7, chornyi2023theoriginof pages 10-11).
Applications / diagnostics / therapeutics	Clinically, ABCD3 is relevant to diagnosis of peroxisomal and bile-acid synthesis disorders, where abnormal DHCA/THCA and related metabolite patterns can point to transporter deficiency. Mechanistic knowledge helps interpret metabolomics/acylcarnitine profiles and distinguish peroxisomal from mitochondrial FAO defects. Structural data may enable future variant interpretation and potentially structure-guided therapeutic development, but no ABCD3-targeted therapy is established yet (chornyi2021peroxisomalmetaboliteand pages 4-6, li2024structuralinsightsinto pages 1-2, ranea‐robles2021theperoxisomaltransporter pages 11-13).
Quantitative stats / data	Reported quantitative data include: ABCD3 ATPase kinetics with Km ~0.24 mM and Vmax ~288.1 nmol Pi/min/mg, versus E596Q mutant Vmax ~107.3 nmol Pi/min/mg; phytanoyl-CoA significantly stimulated ATPase activity (P = 0.0000436). ABCD3 overexpression caused about a 2-fold increase in palmitate β-oxidation in cell studies. In functional lipid-synthesis assays, tracer experiments used 30 μM D3-docosanoic acid (24 h) and 100 μM hexadecanoic acid rescue conditions; plasmalogens were noted to comprise ~18% of human phospholipids (li2024structuralinsightsinto pages 1-2, chornyi2023theoriginof pages 11-12, chornyi2023theoriginof pages 10-11, chornyi2021peroxisomalmetaboliteand pages 4-6).

Table: This table summarizes the core functional annotation of human ABCD3/PMP70, including identity, localization, substrates, pathways, disease links, and recent mechanistic advances. It is useful as a concise evidence-grounded reference for interpreting ABCD3 biology and clinical relevance.

Key visual evidence: Proposed ABCD3 phytanoyl-CoA transport cycle schematic from Li et al. 2024 (li2024structuralinsightsinto media 7540f9ec).

References (URLs and publication dates as available in retrieved evidence)

Li Y. et al. Structural insights into human ABCD3-mediated peroxisomal acyl-CoA translocation. Cell Discovery (Sep 2024). https://doi.org/10.1038/s41421-024-00722-8 (li2024structuralinsightsinto pages 1-2, li2024structuralinsightsinto media 7540f9ec)
Chornyi S. et al. The origin of long-chain fatty acids required for de novo ether lipid/plasmalogen synthesis. Journal of Lipid Research (May 2023). https://doi.org/10.1016/j.jlr.2023.100364 (chornyi2023theoriginof pages 1-2, chornyi2023theoriginof pages 6-7)
Ranea-Robles P. et al. The peroxisomal transporter ABCD3 plays a major role in hepatic dicarboxylic fatty acid metabolism and lipid homeostasis. Journal of Inherited Metabolic Disease (Oct 2021). https://doi.org/10.1002/jimd.12440 (ranea‐robles2021theperoxisomaltransporter pages 11-13)
Tawbeh A. et al. Peroxisomal ABC Transporters: An Update. International Journal of Molecular Sciences (Jun 2021). https://doi.org/10.3390/ijms22116093 (tawbeh2021peroxisomalabctransporters pages 3-4, tawbeh2021peroxisomalabctransporters pages 11-13)
Chornyi S. et al. Peroxisomal Metabolite and Cofactor Transport in Humans. Frontiers in Cell and Developmental Biology (Jan 2021). https://doi.org/10.3389/fcell.2020.613892 (chornyi2021peroxisomalmetaboliteand pages 4-6)
Andreoletti P. et al. Predictive Structure and Topology of Peroxisomal ABC Transporters. International Journal of Molecular Sciences (Jul 2017). https://doi.org/10.3390/ijms18071593 (andreoletti2017predictivestructureand pages 1-3, andreoletti2017predictivestructureand pages 3-5)
Geillon F. et al. Peroxisomal ATP-binding cassette transporters form mainly tetramers. Journal of Biological Chemistry (Apr 2017). https://doi.org/10.1074/jbc.m116.772806 (geillon2017peroxisomalatpbindingcassette pages 11-12, geillon2017peroxisomalatpbindingcassette pages 7-8)
Imanaka T. Biogenesis and Function of Peroxisomes in Human Disease with a Focus on the ABC Transporter. Biological & Pharmaceutical Bulletin (May 2019). https://doi.org/10.1248/bpb.b18-00723 (imanaka2019biogenesisandfunction pages 8-9, imanaka2019biogenesisandfunction pages 9-10)
Kemp S. et al. Mammalian peroxisomal ABC transporters: from endogenous substrates to pathology and clinical significance. British Journal of Pharmacology (Dec 2011). https://doi.org/10.1111/j.1476-5381.2011.01435.x (kemp2011mammalianperoxisomalabc pages 8-9)
Clayton P.T. et al. Treatment of Inborn Errors by Product Replacement: The Example of Inborn Errors of Bile Acid Synthesis. Journal of Inherited Metabolic Disease (Aug 2025). https://doi.org/10.1002/jimd.70081 (clayton2025treatmentofinborn pages 11-12)
Heyliger S. et al. Analysis of Peroxisomal ABCD3 Transporter as a Prognostic Factor in Clear Cell Renal Cell Carcinoma. Cancer Genomics & Proteomics (Aug 2025). https://doi.org/10.21873/cgp.20530 (heyliger2025analysisofperoxisomal pages 7-10)

References

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(chornyi2023theoriginof pages 11-12): Serhii Chornyi, Rob Ofman, Janet Koster, and Hans R. Waterham. The origin of long-chain fatty acids required for de novo ether lipid/plasmalogen synthesis. Journal of Lipid Research, 64:100364, May 2023. URL: https://doi.org/10.1016/j.jlr.2023.100364, doi:10.1016/j.jlr.2023.100364. This article has 17 citations and is from a peer-reviewed journal.
(andreoletti2017predictivestructureand pages 1-3): Pierre Andreoletti, Quentin Raas, Catherine Gondcaille, Mustapha Cherkaoui-Malki, Doriane Trompier, and Stéphane Savary. Predictive structure and topology of peroxisomal atp-binding cassette (abc) transporters. International Journal of Molecular Sciences, 18:1593, Jul 2017. URL: https://doi.org/10.3390/ijms18071593, doi:10.3390/ijms18071593. This article has 21 citations.
(chornyi2023theoriginof pages 10-11): Serhii Chornyi, Rob Ofman, Janet Koster, and Hans R. Waterham. The origin of long-chain fatty acids required for de novo ether lipid/plasmalogen synthesis. Journal of Lipid Research, 64:100364, May 2023. URL: https://doi.org/10.1016/j.jlr.2023.100364, doi:10.1016/j.jlr.2023.100364. This article has 17 citations and is from a peer-reviewed journal.
(geillon2017peroxisomalatpbindingcassette pages 7-8): Flore Geillon, Catherine Gondcaille, Quentin Raas, Alexandre M.M. Dias, Delphine Pecqueur, Caroline Truntzer, Géraldine Lucchi, Patrick Ducoroy, Pierre Falson, Stéphane Savary, and Doriane Trompier. Peroxisomal atp-binding cassette transporters form mainly tetramers. Journal of Biological Chemistry, 292:6965-6977, Apr 2017. URL: https://doi.org/10.1074/jbc.m116.772806, doi:10.1074/jbc.m116.772806. This article has 25 citations and is from a domain leading peer-reviewed journal.

Citations

tawbeh2021peroxisomalabctransporters pages 1-3
chornyi2021peroxisomalmetaboliteand pages 4-6
li2024structuralinsightsinto pages 1-2
tawbeh2021peroxisomalabctransporters pages 3-4
andreoletti2017predictivestructureand pages 3-5
imanaka2019biogenesisandfunction pages 8-9
tawbeh2021peroxisomalabctransporters pages 11-13
imanaka2019biogenesisandfunction pages 9-10
kemp2011mammalianperoxisomalabc pages 8-9
tawbeh2021peroxisomalabctransporters pages 14-16
clayton2025treatmentofinborn pages 11-12
heyliger2025analysisofperoxisomal pages 7-10
chornyi2023theoriginof pages 1-2
morita2012peroxisomalabctransporters pages 2-3
geillon2017peroxisomalatpbindingcassette pages 11-12
chornyi2023theoriginof pages 6-7
morita2012peroxisomalabctransporters pages 3-4
tawbeh2021peroxisomalabctransporters pages 10-11
chornyi2023theoriginof pages 11-12
andreoletti2017predictivestructureand pages 1-3
chornyi2023theoriginof pages 10-11
geillon2017peroxisomalatpbindingcassette pages 7-8
https://doi.org/10.1038/s41421-024-00722-8
https://doi.org/10.1002/jimd.12440
https://doi.org/10.1016/j.jlr.2023.100364
https://doi.org/10.1002/jimd.70081
https://doi.org/10.21873/cgp.20530
https://doi.org/10.3390/ijms22116093
https://doi.org/10.3389/fcell.2020.613892
https://doi.org/10.3390/ijms18071593
https://doi.org/10.1074/jbc.m116.772806
https://doi.org/10.1248/bpb.b18-00723
https://doi.org/10.1111/j.1476-5381.2011.01435.x
https://doi.org/10.1016/j.bbadis.2012.02.009,
https://doi.org/10.3390/ijms22116093,
https://doi.org/10.3390/ijms18071593,
https://doi.org/10.1074/jbc.m116.772806,
https://doi.org/10.1038/s41421-024-00722-8,
https://doi.org/10.3389/fcell.2020.613892,
https://doi.org/10.1002/jimd.12440,
https://doi.org/10.1248/bpb.b18-00723,
https://doi.org/10.1016/j.jlr.2023.100364,
https://doi.org/10.1111/j.1476-5381.2011.01435.x,
https://doi.org/10.1002/jimd.70081,
https://doi.org/10.21873/cgp.20530,

📚 Additional Documentation

Notes

(ABCD3-notes.md)

ABCD3 (PMP70) Research Notes

Gene Overview

ABCD3 (ATP-binding cassette sub-family D member 3), also known as PMP70, is a peroxisomal ABC half-transporter that forms homodimers to catalyze ATP-dependent import of fatty acid substrates into peroxisomes for beta-oxidation.

Key Literature Findings

Substrate Specificity

ABCD3 has broad substrate specificity, preferring hydrophilic substrates: long-chain unsaturated fatty acids, branched-chain fatty acids (pristanic acid), dicarboxylic acids, and bile acid CoA-esters PMID:24333844
Substrate specificity overlaps with ABCD1 and ABCD2, but ABCD3 is distinct in preferring hydrophilic substrates PMID:24333844
Each half-transporter can function as a homodimer PMID:24333844

Bile Acid Transport - Critical Evidence

ABCD3-deficient patient: accumulation of peroxisomal C27-bile acid intermediates (DHCA, THCA) in plasma, establishing ABCD3 role in bile acid biosynthesis PMID:25168382
Abcd3 knockout mice: accumulation of phytanic acid after phytol loading; reduction of C24 bile acids with increased C27 bile acid intermediates PMID:25168382
This causes CBAS5 (Congenital bile acid synthesis defect 5) PMID:25168382
NOTE: The bile acid transport evidence is primarily from patient/mouse studies (loss-of-function), not direct in vitro transport assays with bile acid substrates

Dicarboxylic Acid Transport

Abcd3 knockout mice show increased hepatic long-chain DCAs (C14-C18) and urinary medium-chain DCAs PMID:34564857
Knockout mice show hepatomegaly, lipodystrophy, elevated C27 bile acid precursors PMID:34564857

ATPase and Thioesterase Activities

Purified NBF of PMP70: KM for ATP = 8.2 uM; ATP-specific, no GTPase activity PMID:11248239
G478R mutation decreased ATP binding; S572I decreased ATPase activity PMID:11248239
Reconstituted in proteoliposomes: displays stable ATPase activity (inhibited by AlF3) and acyl-CoA thioesterase activity PMID:29397936

Cryo-EM Structural Studies

Xu et al. 2024 (PMID:39223112) - Cell Discovery
Two cryo-EM structures: phytanoyl-CoA-bound (2.9 A) and ATP-bound (3.2 A)
Inward-facing (substrate-bound) and outward-facing (ATP-bound) conformations
Two phytanoyl-CoA molecules bind individually to each TMD (distinct from ABCD1)
Bile acid intermediates DHCA-CoA and THCA-CoA are ABCD3-specific substrates
ATP binding causes "scissor-like movement" expanding translocation cavity exit by ~13.7 A
PDB: 8Z0F, 8Z9X
2025 PNAS paper (PMID:40501884)
Full-length ABCD3: apo (3.33 A) and phytanoyl-CoA-bound (3.13 A) structures
Both inward-facing conformations
Substrate binding induces ~5-fold increase in ATPase activity
Substrate binding reduces NBD separation (38.18 to 34.28 A)
Proposed cycle: substrate binding -> NBD closure -> ATP binding -> outward-open -> substrate release -> ATP hydrolysis -> reset

Direct Evidence for ATP-dependent Bile Acid Transport

The Xu et al. 2024 cryo-EM paper (PMID:39223112) tested bile acid intermediates DHCA-CoA and THCA-CoA and found them to be ABCD3-specific substrates
However, the primary in vivo evidence comes from loss-of-function studies (patient + KO mice) showing bile acid intermediate accumulation PMID:25168382
Direct in vitro reconstitution assays demonstrating ATP-dependent transport of bile salt CoA esters specifically by ABCD3 proteoliposomes have not been published as of this review

Dimerization and Interactions

Forms homodimers (FRET microscopy) PMID:17609205
Can form heterodimers with ABCD1 and ABCD2 [PMID:10551832, PMID:17609205]
Interacts with PEX19 for peroxisomal targeting [PMID:10704444, PMID:16344115, PMID:17761678]

Peroxisome Organization

Overexpression of PMP70 can suppress PEX2 deficiency and restore peroxisome biogenesis [PMID:9425230, PMID:9765053]
This likely reflects the importance of ABC transporters in peroxisomal membrane organization

Key Questions for Review

Is "fatty acid biosynthetic process" (GO:0006633) annotated via PMID:25168382 appropriate? The paper describes bile acid biosynthesis defect, not fatty acid biosynthesis per se.
"Peroxisomal matrix" localization (GO:0005782) - ABCD3 is a transmembrane protein; matrix localization seems incorrect unless referring to the NBD domain orientation.
Multiple "protein binding" (GO:0005515) annotations - per curation guidelines, these are uninformative and should be replaced with specific binding terms.
"Identical protein binding" (GO:0042802) via IEA - should be replaced by the IDA-supported "protein homodimerization activity" annotation.
Mitochondrial localization (GO:0005739) - IEA transferred from rat; ABCD3 is well-established as peroxisomal.

📄 View Raw YAML

id: P28288
gene_symbol: ABCD3
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: ABCD3 (PMP70) is a peroxisomal ABC half-transporter that homodimerizes to form an active
  ATP-dependent transporter catalyzing import of fatty acid substrates into peroxisomes for beta-oxidation.
  It has broad substrate specificity, preferring hydrophilic substrates including long-chain unsaturated
  fatty acids, branched-chain fatty acids (pristanic acid), dicarboxylic acids, and bile acid CoA-esters.
  ABCD3 possesses intrinsic fatty acyl-CoA thioesterase activity and ATPase activity. Loss of ABCD3 causes
  congenital bile acid synthesis defect type 5 (CBAS5), characterized by accumulation of C27-bile acid
  intermediates. Recent cryo-EM structures reveal an alternating-access transport mechanism with substrate-induced
  NBD dimerization driving conformational changes from inward-open to outward-open states.
alternative_products:
- name: '1'
  id: P28288-1
- name: '2'
  id: P28288-2
  sequence_note: VSP_031189
- name: '3'
  id: P28288-3
  sequence_note: VSP_031187, VSP_031188
existing_annotations:
- term:
    id: GO:0042626
    label: ATPase-coupled transmembrane transporter activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: ABCD3 is an established ATP-dependent peroxisomal membrane transporter. IBA annotation is
      phylogenetically sound and well-supported by direct experimental data from proteoliposome reconstitution
      studies [PMID:29397936] and yeast complementation assays [PMID:24333844].
    action: ACCEPT
    reason: Core molecular function of ABCD3, supported by multiple lines of experimental evidence including
      ATPase activity measurements and substrate transport assays.
    supported_by:
    - reference_id: PMID:29397936
      supporting_text: ABCD1-4 displayed stable ATPase activity, which was inhibited by AlF3
    - reference_id: PMID:24333844
      supporting_text: the phenotype of the pxa1/pxa2Delta yeast mutant, i.e. impaired oxidation of oleic
        acid, cannot only be partially rescued by HsABCD1, HsABCD2, but also by HsABCD3
- term:
    id: GO:0005324
    label: long-chain fatty acid transmembrane transporter activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: ABCD3 transports long-chain fatty acids across the peroxisomal membrane. Demonstrated by
      yeast complementation showing rescue of fatty acid oxidation defects [PMID:24333844] and supported
      by loss-of-function studies in knockout mice [PMID:34564857].
    action: ACCEPT
    reason: Core function. IBA annotation is well-supported by IMP evidence from van Roermund et al. showing
      ABCD3 can partially rescue oleic acid oxidation in yeast mutants.
    supported_by:
    - reference_id: PMID:24333844
      supporting_text: most hydrophilic substrates like long-chain unsaturated-, long branched-chain-
        and long-chain dicarboxylic fatty acids by HsABCD3
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: ABCD3 is a well-established peroxisomal membrane protein, demonstrated by immunofluorescence
      and FRET microscopy in multiple studies [PMID:17609205, PMID:17761678, PMID:10704444].
    action: ACCEPT
    reason: 'Core localization. Extensively validated by multiple experimental methods including immunofluorescence,
      FRET, and cryo-EM structures (PDB: 8Z0F, 8Z9X).'
    supported_by:
    - reference_id: PMID:17609205
      supporting_text: ALDP and PMP70 form homodimers as well as ALDP/PMP70 heterodimers
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: ABCD3 facilitates import of fatty acid substrates into peroxisomes for beta-oxidation. Supported
      by yeast complementation studies [PMID:24333844] and overexpression rescue of VLCFA beta-oxidation
      defects [PMID:9425230].
    action: ACCEPT
    reason: Core biological process. ABCD3 imports substrates destined for peroxisomal beta-oxidation.
      IBA is phylogenetically sound and experimentally validated.
    supported_by:
    - reference_id: PMID:24333844
      supporting_text: the phenotype of the pxa1/pxa2Delta yeast mutant, i.e. impaired oxidation of oleic
        acid, cannot only be partially rescued by HsABCD1, HsABCD2, but also by HsABCD3
    - reference_id: PMID:9425230
      supporting_text: Expression of either ALDP or PMP70 restores VLCFA beta-oxidation in X-ALD fibroblasts,
        indicating overlapping functions
- term:
    id: GO:0015910
    label: long-chain fatty acid import into peroxisome
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: ABCD3 imports long-chain fatty acids into peroxisomes as CoA esters. Supported by yeast complementation
      [PMID:24333844] and ABCD3-deficient patient data [PMID:25168382].
    action: ACCEPT
    reason: Core function of ABCD3. Phylogenetically conserved and experimentally validated.
    supported_by:
    - reference_id: PMID:24333844
      supporting_text: All these fatty acids are most likely transported as CoA esters
- term:
    id: GO:0042760
    label: very long-chain fatty acid catabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: ABCD3 contributes to VLCFA catabolism by importing substrates for peroxisomal beta-oxidation.
      Supported by IGI evidence from ABCD1/ABCD3 co-expression studies [PMID:9425230], though ABCD1 is
      the primary VLCFA transporter.
    action: KEEP_AS_NON_CORE
    reason: ABCD3 contributes to VLCFA catabolism but is not the primary transporter for VLCFAs. ABCD1
      preferentially handles the most hydrophobic VLCFAs (C24:0, C26:0) [PMID:24333844]. ABCD3 prefers
      more hydrophilic substrates. The Ferdinandusse et al. patient showed normal C26:0 beta-oxidation
      despite ABCD3 deficiency [PMID:25168382].
    supported_by:
    - reference_id: PMID:25168382
      supporting_text: Peroxisomal beta-oxidation of C26:0 was normal, but beta-oxidation of pristanic
        acid was reduced
    - reference_id: PMID:24333844
      supporting_text: most hydrophobic C24:0 and C26:0 fatty acids are preferentially transported by
        HsABCD1
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: ABCD3 binds ATP via its nucleotide binding fold. Directly demonstrated by purified NBF studies
      with KM of 8.2 uM for ATP [PMID:11248239].
    action: ACCEPT
    reason: Core function, essential for transport activity. Phylogenetically conserved ABC transporter
      feature with direct experimental validation.
    supported_by:
    - reference_id: PMID:11248239
      supporting_text: Both proteins act as an ATP specific binding subunit releasing ADP after ATP hydrolysis
- term:
    id: GO:0007031
    label: peroxisome organization
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: ABCD3 overexpression can rescue peroxisome biogenesis defects in PEX2-deficient cells [PMID:9425230,
      PMID:9765053]. This likely reflects its role as a major peroxisomal membrane component rather than
      a direct organizer of peroxisome biogenesis.
    action: KEEP_AS_NON_CORE
    reason: Not a core function. The effect on peroxisome organization is indirect, reflecting ABCD3's
      abundance in the peroxisomal membrane rather than a direct role in peroxisome biogenesis.
    supported_by:
    - reference_id: PMID:9425230
      supporting_text: Their expression also restores peroxisome biogenesis in cells that are deficient
        in the peroxisomal membrane protein Pex2p
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA transfer from rat ortholog. ABCD3 is overwhelmingly established as a peroxisomal membrane
      protein. The N-terminal 80aa segment of PMP70, when expressed alone, can target to the outer mitochondrial
      membrane [PMID:20007743], but full-length PMP70 localizes exclusively to peroxisomes. This IEA annotation
      is misleading.
    action: REMOVE
    reason: ABCD3 is a peroxisomal protein. While an isolated N-terminal fragment can mis-target to mitochondria
      [PMID:20007743], this is an artifact of truncation, not physiological localization. No full-length
      ABCD3 has been demonstrated in mitochondria.
    supported_by:
    - reference_id: PMID:20007743
      supporting_text: When the N80-segment was fused to EGFP, the fusion protein was targeted to the
        outer mitochondrial membrane... The full-length PMP70 molecule was clearly located in the ER in
        the absence of the N80-segment
- term:
    id: GO:0006699
    label: bile acid biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: ABCD3 imports C27-bile acid intermediates into peroxisomes for side-chain shortening, a critical
      step in bile acid biosynthesis. Loss of ABCD3 causes CBAS5 with accumulation of C27-bile acid intermediates
      [PMID:25168382].
    action: ACCEPT
    reason: Well-supported by patient data and knockout mouse studies. ABCD3 transports bile acid CoA-esters
      (DHCA-CoA, THCA-CoA) into peroxisomes for conversion to mature C24 bile acids.
    supported_by:
    - reference_id: PMID:25168382
      supporting_text: ABCD3 is involved in transport of branched-chain fatty acids and C27 bile acids
        into the peroxisome and that this is a crucial step in bile acid biosynthesis
- term:
    id: GO:0006869
    label: lipid transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: ABCD3 transports lipid substrates (fatty acids, bile acid intermediates) across the peroxisomal
      membrane. This is a correct but very general annotation.
    action: ACCEPT
    reason: Correct but general. More specific terms (GO:0015910, GO:0015721) are also annotated and provide
      more precise functional description. Acceptable as a broader IEA annotation.
- term:
    id: GO:0009410
    label: response to xenobiotic stimulus
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: IEA transfer from rat ortholog. In rat, PMP70 expression may be upregulated by peroxisome
      proliferators (xenobiotics), but this is a transcriptional response, not a direct function of the
      ABCD3 protein itself.
    action: MARK_AS_OVER_ANNOTATED
    reason: Transcriptional upregulation by xenobiotics reflects regulatory biology, not a direct function
      of the ABCD3 protein. This annotation conflates gene regulation with protein function.
- term:
    id: GO:0015721
    label: bile acid and bile salt transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: ABCD3 transports C27-bile acid CoA-ester intermediates (DHCA-CoA, THCA-CoA) into peroxisomes.
      Loss of ABCD3 leads to accumulation of these intermediates [PMID:25168382]. Cryo-EM studies confirm
      bile acid intermediates as ABCD3-specific substrates [PMID:39223112].
    action: ACCEPT
    reason: Well-supported by patient genetics, knockout mice, and structural studies. DHCA-CoA and THCA-CoA
      are ABCD3-specific substrates per cryo-EM data.
    supported_by:
    - reference_id: PMID:25168382
      supporting_text: ABCD3 is involved in transport of branched-chain fatty acids and C27 bile acids
        into the peroxisome
- term:
    id: GO:0042802
    label: identical protein binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: ABCD3 forms homodimers, demonstrated by FRET microscopy in living cells [PMID:17609205].
      However, the more specific term GO:0042803 (protein homodimerization activity) is already annotated
      with IDA evidence. This IEA annotation is redundant and less informative.
    action: MODIFY
    reason: The more specific GO:0042803 (protein homodimerization activity) is already annotated with
      direct experimental evidence (IDA, PMID:17609205). This IEA term is less precise.
    proposed_replacement_terms:
    - id: GO:0042803
      label: protein homodimerization activity
- term:
    id: GO:1903512
    label: phytanic acid metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: ABCD3 imports branched-chain fatty acids including pristanic acid (the alpha-oxidation product
      of phytanic acid) into peroxisomes. Abcd3 knockout mice accumulate phytanic acid after phytol loading
      [PMID:25168382]. The ABCD3-deficient patient showed reduced pristanic acid beta-oxidation [PMID:25168382].
    action: ACCEPT
    reason: Supported by knockout mouse and patient data showing impaired branched-chain fatty acid metabolism
      when ABCD3 is absent.
    supported_by:
    - reference_id: PMID:25168382
      supporting_text: Abcd3-/- mice accumulated the branched chain fatty acid phytanic acid after phytol
        loading
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10551832
  review:
    summary: Demonstrates heterodimerization of ABCD3 (PMP70) with ABCD1 (ALDP) by yeast two-hybrid and
      co-immunoprecipitation [PMID:10551832]. Per curation guidelines, 'protein binding' is uninformative;
      a more specific term should be used.
    action: MODIFY
    reason: The interaction with ABCD1 is well-established but 'protein binding' is uninformative. Should
      be annotated with a more specific term reflecting heterodimerization.
    proposed_replacement_terms:
    - id: GO:0046982
      label: protein heterodimerization activity
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10704444
  review:
    summary: Demonstrates interaction of ABCD3 with PEX19, which is required for targeting ABCD3 to peroxisomes
      [PMID:10704444]. PEX19 is a cytosolic chaperone/import receptor for class I peroxisomal membrane
      proteins, of which ABCD3 is a client.
    action: MODIFY
    reason: Specific interaction with PEX19 (a peroxisomal biogenesis chaperone/import receptor) is well-characterized
      but 'protein binding' is uninformative. PEX19 is a distinct protein (not ABCD3 itself), so homo-/heterodimerization
      terms are inappropriate. ABCD3 binds PEX19 as a client of this chaperone, so a chaperone-binding term
      is the more informative molecular function.
    proposed_replacement_terms:
    - id: GO:0051087
      label: protein-folding chaperone binding
    additional_reference_ids:
    - PMID:16344115
    - PMID:17761678
    supported_by:
    - reference_id: PMID:10704444
      supporting_text: PEX19 binds multiple peroxisomal membrane proteins, is predominantly cytoplasmic,
        and is required for peroxisome membrane synthesis
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:14709540
  review:
    summary: PEX19 acts as a cytosolic chaperone and import receptor for class 1 peroxisomal membrane
      proteins including ABCD3 [PMID:14709540]. Duplicates the PEX19 interaction from other entries.
    action: REMOVE
    reason: Uninformative 'protein binding' annotation. The PEX19 interaction is already captured by other
      annotations. Per curation guidelines, protein binding should be avoided.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21102411
  review:
    summary: Structural basis for PEX19/PEX3 docking [PMID:21102411]. ABCD3 is one of many PEX19 cargo
      proteins studied. Again, 'protein binding' is uninformative.
    action: REMOVE
    reason: Uninformative 'protein binding' annotation. The PEX19 interaction is well-covered by other
      annotations. Per curation guidelines, protein binding should be avoided.
- term:
    id: GO:0005324
    label: long-chain fatty acid transmembrane transporter activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: InterPro-based annotation from IPR005283 (fatty acid transporter). Correct and consistent
      with experimental evidence from yeast complementation [PMID:24333844].
    action: ACCEPT
    reason: Correct IEA annotation consistent with IBA and experimental annotations for same term.
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Combined automated annotation. ATP binding is well-established for ABCD3 with IDA evidence
      [PMID:11248239, KM = 8.2 uM].
    action: ACCEPT
    reason: Consistent with experimentally validated annotations.
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Combined automated annotation for peroxisomal localization. Well-supported by extensive experimental
      evidence.
    action: ACCEPT
    reason: Consistent with multiple IDA annotations for peroxisomal localization.
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Combined automated annotation for peroxisomal membrane localization.
    action: ACCEPT
    reason: Consistent with extensive experimental evidence for peroxisomal membrane localization.
- term:
    id: GO:0015910
    label: long-chain fatty acid import into peroxisome
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: InterPro-based annotation. Consistent with IMP evidence from yeast complementation [PMID:24333844].
    action: ACCEPT
    reason: Consistent with experimental annotations.
- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: Generic membrane annotation from InterPro. Correct but very general; more specific peroxisomal
      membrane annotations exist.
    action: ACCEPT
    reason: Correct but very general. Acceptable as a broad IEA annotation alongside more specific peroxisomal
      membrane annotations.
- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: InterPro-based annotation. Consistent with IDA evidence from NBF studies [PMID:11248239]
      and proteoliposome reconstitution [PMID:29397936].
    action: ACCEPT
    reason: Consistent with experimental annotations.
- term:
    id: GO:0042626
    label: ATPase-coupled transmembrane transporter activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: InterPro-based annotation. Consistent with IDA evidence from proteoliposome studies [PMID:29397936].
    action: ACCEPT
    reason: Consistent with IDA annotation for same term.
- term:
    id: GO:0055085
    label: transmembrane transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: Generic transmembrane transport annotation. Correct but very general.
    action: ACCEPT
    reason: Correct but general. More specific transport process terms are also annotated.
- term:
    id: GO:0140359
    label: ABC-type transporter activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: InterPro-based annotation reflecting ABC transporter domain architecture. ABCD3 is indeed
      a member of the ABCD family of ABC transporters.
    action: ACCEPT
    reason: Correct classification. ABCD3 belongs to the ABC transporter superfamily, ABCD family.
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  review:
    summary: HPA immunofluorescence data confirming peroxisomal localization of ABCD3.
    action: ACCEPT
    reason: Core localization, independently validated by multiple methods.
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-382575
  review:
    summary: 'Reactome pathway: ABCD1-3 dimers transfer LCFAs from cytosol to peroxisomal matrix. Consistent
      with ABCD3 function.'
    action: ACCEPT
    reason: Consistent with established localization and function.
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-382613
  review:
    summary: 'Reactome pathway: PEX19 docks ABCD3 to peroxisomal membrane.'
    action: ACCEPT
    reason: Consistent with PEX19-mediated targeting of ABCD3 to peroxisomes.
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9603775
  review:
    summary: 'Reactome pathway: PEX3:PEX19:class I PMP dissociates. ABCD3 is a class I PMP.'
    action: ACCEPT
    reason: Consistent with peroxisomal membrane protein import pathway.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-382613
  review:
    summary: 'Reactome: PEX19 docks ABCD3 to peroxisomal membrane, implying ABCD3 transits through cytosol
      during biogenesis. ABCD3 is synthesized on free ribosomes and targeted posttranslationally [PMID:17761678].'
    action: KEEP_AS_NON_CORE
    reason: ABCD3 passes through the cytosol during posttranslational targeting but its steady-state localization
      is peroxisomal membrane. Cytosol is a transient location during biogenesis, not the functional site.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9603775
  review:
    summary: 'Reactome: PEX3:PEX19:class I PMP complex dissociation. Transient cytosolic location during
      import pathway.'
    action: KEEP_AS_NON_CORE
    reason: Transient localization during biogenesis, not functional site.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9603784
  review:
    summary: 'Reactome: PEX19:class I PMP binds PEX3. Part of peroxisomal membrane protein import.'
    action: KEEP_AS_NON_CORE
    reason: Transient localization during biogenesis.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9603804
  review:
    summary: 'Reactome: PEX19 binds class I peroxisomal membrane proteins in cytosol.'
    action: KEEP_AS_NON_CORE
    reason: Transient localization during biogenesis.
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: EXP
  original_reference_id: PMID:10704444
  review:
    summary: PEX19 binds ABCD3 and is required for its localization to peroxisomal membrane [PMID:10704444].
      Subcellular fractionation and immunofluorescence confirm peroxisomal membrane localization.
    action: ACCEPT
    reason: Core localization with direct experimental evidence from subcellular fractionation and immunofluorescence.
    supported_by:
    - reference_id: PMID:10704444
      supporting_text: PEX19 binds multiple peroxisomal membrane proteins, is predominantly cytoplasmic,
        and is required for peroxisome membrane synthesis
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: EXP
  original_reference_id: PMID:16344115
  review:
    summary: PEX19 mediates targeting of PMP70 to peroxisomes [PMID:16344115]. Confirms peroxisomal membrane
      localization through PEX19 binding studies.
    action: ACCEPT
    reason: Core localization confirmed by PEX19 interaction and targeting studies.
    supported_by:
    - reference_id: PMID:16344115
      supporting_text: Role of Pex19p in the targeting of PMP70 to peroxisome
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: EXP
  original_reference_id: PMID:17761678
  review:
    summary: Hydrophobic regions adjacent to TMDs 1 and 5 are required for PMP70 targeting to peroxisomal
      membrane [PMID:17761678]. Mutagenesis of targeting signals (L21Q/L22Q/L23Q, I70N/L71Q, I307A/L308A)
      abolishes peroxisomal localization.
    action: ACCEPT
    reason: Core localization. Detailed targeting signal mapping confirms peroxisomal membrane as the
      destination.
    supported_by:
    - reference_id: PMID:17761678
      supporting_text: PMP70 possesses two distinct targeting signals, and hydrophobic regions adjacent
        to the first TMD of each region are important for targeting
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: EXP
  original_reference_id: PMID:24333844
  review:
    summary: Subcellular fractionation and functional studies in yeast confirm ABCD3 localizes to peroxisomal
      membrane [PMID:24333844].
    action: ACCEPT
    reason: Core localization confirmed in context of substrate transport studies.
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: EXP
  original_reference_id: PMID:29397936
  review:
    summary: ABCD3 reconstituted into proteoliposomes for functional studies, confirming membrane protein
      nature [PMID:29397936].
    action: ACCEPT
    reason: Core localization confirmed in proteoliposome reconstitution.
- term:
    id: GO:0052817
    label: very long-chain fatty acyl-CoA hydrolase activity
  evidence_type: EXP
  original_reference_id: PMID:29397936
  review:
    summary: ABCD3 reconstituted in proteoliposomes displays acyl-CoA thioesterase activity, cleaving
      fatty acyl-CoA into free fatty acid and CoA [PMID:29397936]. This activity is shared by ABCD1-4.
    action: ACCEPT
    reason: Directly demonstrated in purified reconstituted system. The thioesterase activity is proposed
      to hydrolyze fatty acyl-CoAs prior to ATP-dependent transport.
    supported_by:
    - reference_id: PMID:29397936
      supporting_text: ABCD1-4 were found to possess an equal levels of acyl-CoA thioesterase activity
- term:
    id: GO:0005324
    label: long-chain fatty acid transmembrane transporter activity
  evidence_type: IMP
  original_reference_id: PMID:24333844
  review:
    summary: Expression of human ABCD3 in pxa1/pxa2-delta yeast mutants partially rescues fatty acid oxidation,
      demonstrating transporter function [PMID:24333844]. ABCD3 preferentially transports hydrophilic
      substrates including long-chain unsaturated fatty acids.
    action: ACCEPT
    reason: Core function demonstrated by yeast complementation assay. Key evidence for substrate specificity
      of ABCD3.
    supported_by:
    - reference_id: PMID:24333844
      supporting_text: most hydrophilic substrates like long-chain unsaturated-, long branched-chain-
        and long-chain dicarboxylic fatty acids by HsABCD3
- term:
    id: GO:0006699
    label: bile acid biosynthetic process
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: ISS from mouse ortholog P55096. Well-supported by ABCD3-deficient patient showing accumulation
      of C27-bile acid intermediates [PMID:25168382] and Abcd3 KO mice with reduced C24 bile acids and
      increased C27 intermediates [PMID:25168382, PMID:34564857].
    action: ACCEPT
    reason: Core function. ABCD3 imports bile acid CoA-ester intermediates into peroxisomes for side-chain
      shortening, an essential step in bile acid biosynthesis.
    supported_by:
    - reference_id: PMID:25168382
      supporting_text: ABCD3 is involved in transport of branched-chain fatty acids and C27 bile acids
        into the peroxisome and that this is a crucial step in bile acid biosynthesis
- term:
    id: GO:0015721
    label: bile acid and bile salt transport
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: ISS from mouse ortholog. ABCD3 transports bile acid CoA-ester intermediates (DHCA-CoA, THCA-CoA)
      into peroxisomes. Supported by human genetics [PMID:25168382] and cryo-EM structural data showing
      these are ABCD3-specific substrates [PMID:39223112].
    action: ACCEPT
    reason: Core function. DHCA-CoA and THCA-CoA are ABCD3-specific substrates per cryo-EM data. In vivo
      loss-of-function confirms bile acid transport role.
    supported_by:
    - reference_id: PMID:25168382
      supporting_text: both in the patient and in Abcd3-/- mice, there was evidence of a bile acid biosynthesis
        defect
- term:
    id: GO:0015910
    label: long-chain fatty acid import into peroxisome
  evidence_type: IMP
  original_reference_id: PMID:24333844
  review:
    summary: ABCD3 expression in pxa1/pxa2-delta yeast rescues fatty acid oxidation, demonstrating import
      of long-chain fatty acids into peroxisomes [PMID:24333844].
    action: ACCEPT
    reason: Core function with direct IMP evidence.
    supported_by:
    - reference_id: PMID:24333844
      supporting_text: the phenotype of the pxa1/pxa2Delta yeast mutant, i.e. impaired oxidation of oleic
        acid, cannot only be partially rescued by HsABCD1, HsABCD2, but also by HsABCD3
- term:
    id: GO:1903512
    label: phytanic acid metabolic process
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: ISS from mouse ortholog. ABCD3 imports pristanic acid (and by extension contributes to phytanic
      acid metabolism) into peroxisomes. Abcd3 KO mice accumulate phytanic acid [PMID:25168382].
    action: ACCEPT
    reason: Well-supported by knockout mouse data and patient studies showing reduced pristanic acid beta-oxidation.
    supported_by:
    - reference_id: PMID:25168382
      supporting_text: Abcd3-/- mice accumulated the branched chain fatty acid phytanic acid after phytol
        loading
- term:
    id: GO:0000038
    label: very long-chain fatty acid metabolic process
  evidence_type: IDA
  original_reference_id: PMID:29397936
  review:
    summary: ABCD3 reconstituted in proteoliposomes demonstrates thioesterase and ATPase activities with
      fatty acyl-CoA substrates [PMID:29397936], contributing to VLCFA metabolism.
    action: KEEP_AS_NON_CORE
    reason: ABCD3 can process VLCFAs but this is not its primary substrate preference. ABCD1 is the main
      VLCFA transporter. The ABCD3-deficient patient had normal C26:0 beta-oxidation [PMID:25168382],
      indicating ABCD3 is not essential for VLCFA catabolism.
    supported_by:
    - reference_id: PMID:25168382
      supporting_text: Peroxisomal beta-oxidation of C26:0 was normal
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:24333844
  review:
    summary: Subcellular fractionation confirms ABCD3 localization to peroxisomes [PMID:24333844].
    action: ACCEPT
    reason: Core localization.
- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IDA
  original_reference_id: PMID:11248239
  review:
    summary: Purified nucleotide binding fold (NBF) of PMP70 hydrolyzes ATP (KM = 8.2 uM). ATP-specific,
      no GTPase activity. Mutations G478R and S572I alter ATPase activity [PMID:11248239].
    action: ACCEPT
    reason: Core activity. Direct biochemical demonstration with purified protein.
    supported_by:
    - reference_id: PMID:11248239
      supporting_text: Both proteins act as an ATP specific binding subunit releasing ADP after ATP hydrolysis;
        they did not exhibit GTPase activity
- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IDA
  original_reference_id: PMID:29397936
  review:
    summary: ABCD3 reconstituted in proteoliposomes displays stable ATPase activity inhibited by AlF3
      [PMID:29397936], confirming the NBF study findings in a full-length protein context.
    action: ACCEPT
    reason: Core activity confirmed in full-length reconstituted protein.
    supported_by:
    - reference_id: PMID:29397936
      supporting_text: ABCD1-4 displayed stable ATPase activity, which was inhibited by AlF3
- term:
    id: GO:0042626
    label: ATPase-coupled transmembrane transporter activity
  evidence_type: IDA
  original_reference_id: PMID:29397936
  review:
    summary: Proteoliposome reconstitution demonstrates coupled ATPase-transport activity of ABCD3 [PMID:29397936].
      Cryo-EM structures capture the conformational cycle linking ATP hydrolysis to substrate translocation
      [PMID:39223112].
    action: ACCEPT
    reason: Core molecular function. Direct demonstration in reconstituted system with structural validation
      of the transport mechanism.
    supported_by:
    - reference_id: PMID:29397936
      supporting_text: ABCD1-3 are located on peroxisomal membrane and play an important role in the transportation
        of various fatty acid-CoA derivatives
- term:
    id: GO:0047617
    label: fatty acyl-CoA hydrolase activity
  evidence_type: IDA
  original_reference_id: PMID:29397936
  review:
    summary: ABCD3 possesses intrinsic acyl-CoA thioesterase activity demonstrated in proteoliposomes
      [PMID:29397936]. This activity may hydrolyze fatty acyl-CoAs to free fatty acids prior to transport,
      though the cryo-EM studies suggest intact CoA-esters may also be transported.
    action: ACCEPT
    reason: Directly demonstrated enzymatic activity. The biological significance (whether thioesterase
      activity is required for transport or is a side activity) remains under investigation, but the activity
      is real.
    supported_by:
    - reference_id: PMID:29397936
      supporting_text: ABCD1-4 were found to possess an equal levels of acyl-CoA thioesterase activity
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IDA
  original_reference_id: PMID:24333844
  review:
    summary: ABCD3 expression in yeast mutants restores fatty acid beta-oxidation, particularly for hydrophilic
      substrates [PMID:24333844]. Fatty acid oxidation measurements with various substrates reveal distinctive
      substrate preferences.
    action: ACCEPT
    reason: Core function supported by direct biochemical evidence.
    supported_by:
    - reference_id: PMID:24333844
      supporting_text: the phenotype of the pxa1/pxa2Delta yeast mutant, i.e. impaired oxidation of oleic
        acid, cannot only be partially rescued by HsABCD1, HsABCD2, but also by HsABCD3
- term:
    id: GO:0006633
    label: fatty acid biosynthetic process
  evidence_type: IMP
  original_reference_id: PMID:25168382
  review:
    summary: This annotation is problematic. PMID:25168382 describes a bile acid biosynthesis defect in
      an ABCD3-deficient patient, not a fatty acid biosynthesis defect. The patient showed accumulation
      of C27-bile acid intermediates. ABCD3 does not synthesize fatty acids; it imports them for degradation.
      The correct annotation should be GO:0006699 (bile acid biosynthetic process), which is already annotated
      separately.
    action: MODIFY
    reason: PMID:25168382 describes a bile acid biosynthesis defect, not fatty acid biosynthesis. ABCD3
      imports substrates for beta-oxidation (catabolism), not biosynthesis. The KO mice showed altered
      lipogenesis [PMID:34564857] as a secondary metabolic effect, but this is not a direct function of
      ABCD3. The correct term for the primary finding is bile acid biosynthetic process.
    proposed_replacement_terms:
    - id: GO:0006699
      label: bile acid biosynthetic process
    supported_by:
    - reference_id: PMID:25168382
      supporting_text: A novel bile acid biosynthesis defect due to a deficiency of peroxisomal ABCD3
- term:
    id: GO:0016020
    label: membrane
  evidence_type: HDA
  original_reference_id: PMID:19946888
  review:
    summary: High-throughput proteomics identification of ABCD3 in NK cell membrane fractions [PMID:19946888].
      Generic membrane annotation.
    action: ACCEPT
    reason: Correct but very general. ABCD3 is indeed a membrane protein. More specific peroxisomal membrane
      annotations provide better functional context.
- term:
    id: GO:0005782
    label: peroxisomal matrix
  evidence_type: IDA
  original_reference_id: PMID:9765053
  review:
    summary: PMID:9765053 describes restoration of PEX2 peroxisome assembly defects by overexpression
      of PMP70. ABCD3 is a multi-pass transmembrane protein with its NBD domain extending into the cytosol.
      The annotation to peroxisomal matrix is problematic for a transmembrane protein, unless referring
      to the NBD domain facing the matrix side. However, cryo-EM structures show the NBDs are cytosolic
      [PMID:39223112].
    action: REMOVE
    reason: ABCD3 is an integral membrane protein of the peroxisomal membrane with its NBD domain in the
      cytosol. It is not a peroxisomal matrix protein. The cryo-EM structures confirm the cytosolic orientation
      of the NBDs [PMID:39223112]. Peroxisomal matrix annotation is incorrect for this transmembrane protein.
- term:
    id: GO:0007031
    label: peroxisome organization
  evidence_type: IMP
  original_reference_id: PMID:9765053
  review:
    summary: Overexpression of PMP70 restores peroxisome assembly in PEX2-deficient cells [PMID:9765053].
      This is an indirect effect of providing abundant peroxisomal membrane protein.
    action: KEEP_AS_NON_CORE
    reason: Not a direct function. The rescue of peroxisome assembly defects by PMP70 overexpression is
      an indirect compensatory effect, not evidence of a primary role in peroxisome organization.
    supported_by:
    - reference_id: PMID:9765053
      supporting_text: Restoration of PEX2 peroxisome assembly defects by overexpression of PMP70
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:17542813
  review:
    summary: Immunofluorescence study showing ABCD3 localizes to peroxisomes [PMID:17542813]. The paper
      primarily studies ABCD1/ALDP but confirms ABCD3 peroxisomal localization.
    action: ACCEPT
    reason: Core localization confirmed by immunofluorescence.
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:20007743
  review:
    summary: Multiple targeting signals in the N-terminal portion of PMP70 direct it to peroxisomes [PMID:20007743].
      Confirms peroxisomal localization.
    action: ACCEPT
    reason: Core localization.
    supported_by:
    - reference_id: PMID:20007743
      supporting_text: Cooperation of the organelle-targeting signals enables PMP70 to correctly target
        to peroxisomal membranes
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:19479899
  review:
    summary: Pex3p-dependent peroxisomal biogenesis initiates in the ER of human fibroblasts [PMID:19479899].
      ABCD3 used as a peroxisomal marker.
    action: ACCEPT
    reason: Core localization; ABCD3 is routinely used as a peroxisomal marker.
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IGI
  original_reference_id: PMID:9425230
  review:
    summary: Expression of PMP70 restores VLCFA beta-oxidation in X-ALD (ABCD1-deficient) fibroblasts,
      demonstrating overlapping function between ABCD1 and ABCD3 in fatty acid beta-oxidation [PMID:9425230].
    action: ACCEPT
    reason: Core function. IGI evidence from complementation showing ABCD3 can substitute for ABCD1 in
      supporting VLCFA beta-oxidation.
    supported_by:
    - reference_id: PMID:9425230
      supporting_text: Expression of either ALDP or PMP70 restores VLCFA beta-oxidation in X-ALD fibroblasts,
        indicating overlapping functions
- term:
    id: GO:0007031
    label: peroxisome organization
  evidence_type: IDA
  original_reference_id: PMID:9425230
  review:
    summary: ABCD3 expression restores peroxisome biogenesis in PEX2-deficient cells [PMID:9425230]. Indirect
      effect of providing peroxisomal membrane components.
    action: KEEP_AS_NON_CORE
    reason: Not a direct function. Same indirect rescue as PMID:9765053.
    supported_by:
    - reference_id: PMID:9425230
      supporting_text: Their expression also restores peroxisome biogenesis in cells that are deficient
        in the peroxisomal membrane protein Pex2p
- term:
    id: GO:0042760
    label: very long-chain fatty acid catabolic process
  evidence_type: IGI
  original_reference_id: PMID:9425230
  review:
    summary: ABCD3 expression restores VLCFA beta-oxidation in ABCD1-deficient cells [PMID:9425230].
    action: KEEP_AS_NON_CORE
    reason: ABCD3 can contribute to VLCFA catabolism but it is not the primary VLCFA transporter. ABCD1
      handles C24:0/C26:0 preferentially [PMID:24333844]. The ABCD3-deficient patient had normal C26:0
      beta-oxidation [PMID:25168382].
    supported_by:
    - reference_id: PMID:9425230
      supporting_text: Expression of either ALDP or PMP70 restores VLCFA beta-oxidation in X-ALD fibroblasts,
        indicating overlapping functions
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10777694
  review:
    summary: Interaction of ABCD3 with PEX19 demonstrated by various binding assays [PMID:10777694]. Per
      curation guidelines, 'protein binding' is uninformative.
    action: REMOVE
    reason: Uninformative. The PEX19 interaction is functionally relevant for peroxisomal targeting but
      'protein binding' does not capture this. The interaction is already reflected in the peroxisomal
      membrane localization annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:17609205
  review:
    summary: FRET microscopy demonstrating ABCD3 homo- and heterodimerization with ABCD1 in living cells
      [PMID:17609205]. The specific homodimerization function is already annotated as GO:0042803 (protein
      homodimerization activity) with IDA evidence from the same paper.
    action: REMOVE
    reason: Uninformative. The functional interaction is better captured by GO:0042803 (protein homodimerization
      activity) already annotated from this same reference.
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:9425230
  review:
    summary: ABCD3 localizes to peroxisomes [PMID:9425230].
    action: ACCEPT
    reason: Core localization.
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: IDA
  original_reference_id: PMID:17609205
  review:
    summary: FRET microscopy in living cells confirms ABCD3 localization to peroxisomal membrane where
      it forms homodimers [PMID:17609205].
    action: ACCEPT
    reason: Core localization with in vivo FRET confirmation.
    supported_by:
    - reference_id: PMID:17609205
      supporting_text: ALDP and PMP70 form homodimers as well as ALDP/PMP70 heterodimers where ALDP homodimers
        predominate
- term:
    id: GO:0042803
    label: protein homodimerization activity
  evidence_type: IDA
  original_reference_id: PMID:17609205
  review:
    summary: FRET microscopy in living cells demonstrates ABCD3 homodimerization [PMID:17609205]. Dimerization
      is necessary for functional transporter activity. Also supported by cryo-EM structures showing homodimeric
      assembly [PMID:39223112, PMID:40501884].
    action: ACCEPT
    reason: Core function. Half-transporter dimerization is essential for ABC transporter function. Structural
      studies confirm the homodimeric arrangement.
    supported_by:
    - reference_id: PMID:17609205
      supporting_text: We demonstrate in vivo that ALDP and PMP70 form homodimers as well as ALDP/PMP70
        heterodimers
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16344115
  review:
    summary: PEX19 interaction with ABCD3 for peroxisomal targeting [PMID:16344115].
    action: REMOVE
    reason: Uninformative 'protein binding'. The PEX19 interaction is already reflected in peroxisomal
      membrane localization annotations.
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:16344115
  review:
    summary: ABCD3 localization to peroxisomes confirmed in PEX19 targeting studies [PMID:16344115].
    action: ACCEPT
    reason: Core localization.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11453642
  review:
    summary: Targeting elements in the N-terminal part of PMP70 [PMID:11453642]. PEX19 interaction.
    action: REMOVE
    reason: Uninformative 'protein binding'. PEX19 interaction covered elsewhere.
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IDA
  original_reference_id: PMID:11248239
  review:
    summary: Direct measurement of ATP binding by purified NBF of PMP70 with KM = 8.2 uM [PMID:11248239].
      ATP-specific, no GTP binding.
    action: ACCEPT
    reason: Core function with direct biochemical evidence.
    supported_by:
    - reference_id: PMID:11248239
      supporting_text: Both proteins act as an ATP specific binding subunit releasing ADP after ATP hydrolysis
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:11453642
  review:
    summary: ABCD3 localizes to peroxisomes [PMID:11453642].
    action: ACCEPT
    reason: Core localization.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11590176
  review:
    summary: Two different targeting signals direct human PMP22 to peroxisomes [PMID:11590176]. ABCD3
      interaction context. Uninformative term.
    action: REMOVE
    reason: Uninformative 'protein binding'.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11883941
  review:
    summary: PEX19 splice variants and their functions in peroxisomal assembly [PMID:11883941]. ABCD3
      as PEX19 cargo. Uninformative term.
    action: REMOVE
    reason: Uninformative 'protein binding'. PEX19 interaction covered by other annotations.
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:9922452
  review:
    summary: Peroxisome synthesis in the absence of preexisting peroxisomes [PMID:9922452]. ABCD3 used
      as peroxisomal marker.
    action: ACCEPT
    reason: Core localization.
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:10704444
  review:
    summary: ABCD3 localizes to peroxisomes, requires PEX19 for targeting [PMID:10704444].
    action: ACCEPT
    reason: Core localization.
- term:
    id: GO:0015125
    label: bile acid transmembrane transporter activity
  evidence_type: IMP
  original_reference_id: PMID:25168382
  review:
    summary: ABCD3 specifically transports C27-bile acid CoA-ester intermediates (DHCA-CoA, THCA-CoA)
      across the peroxisomal membrane. Loss of ABCD3 causes accumulation of these intermediates in patient
      plasma [PMID:25168382] and in Abcd3 KO mice [PMID:25168382, PMID:34564857]. Cryo-EM structural data
      identifies these bile acid intermediates as ABCD3-specific substrates [PMID:39223112]. The existing
      annotations capture the bile acid transport process (GO:0015721) but no molecular function term for
      bile acid transporter activity is present.
    action: NEW
    reason: ABCD3 catalyzes transmembrane transport of bile acid CoA-esters across the peroxisomal membrane.
      The existing process annotation GO:0015721 (bile acid and bile salt transport) covers the broader
      biological process. This molecular function term captures the direct transporter activity and is supported
      by patient genetics, KO mice, and cryo-EM substrate-binding data.
    supported_by:
    - reference_id: PMID:25168382
      supporting_text: ABCD3 is involved in transport of branched-chain fatty acids and C27 bile acids
        into the peroxisome
- term:
    id: GO:0046982
    label: protein heterodimerization activity
  evidence_type: IDA
  original_reference_id: PMID:17609205
  review:
    summary: ABCD3 forms heterodimers with ABCD1 and ABCD2, demonstrated by FRET microscopy in living
      cells [PMID:17609205] and by yeast two-hybrid and co-immunoprecipitation [PMID:10551832]. This is
      a more informative annotation than the generic 'protein binding' currently annotated for the ABCD1/ABCD3
      interaction.
    action: NEW
    reason: Replaces uninformative 'protein binding' annotations. ABCD3 heterodimerization with ABCD1
      is well-established and functionally relevant, as it creates transporters with potentially different
      substrate preferences.
    supported_by:
    - reference_id: PMID:17609205
      supporting_text: We demonstrate in vivo that ALDP and PMP70 form homodimers as well as ALDP/PMP70
        heterodimers
    - reference_id: PMID:10551832
      supporting_text: Co-immunoprecipitation demonstrated the homodimerization of ALDP, the heterodimerization
        of ALDP with PMP70
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator
    judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl
    Compara
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:9425230
  title: Suppression of peroxisomal membrane protein defects by peroxisomal ATP binding cassette (ABC)
    proteins.
  findings:
  - statement: Expression of PMP70 restores VLCFA beta-oxidation in X-ALD fibroblasts
  - statement: PMP70 and ALDP expression restores peroxisome biogenesis in PEX2-deficient cells
  - statement: Indicates overlapping functions between peroxisomal ABC transporters
- id: PMID:9765053
  title: Restoration of PEX2 peroxisome assembly defects by overexpression of PMP70.
  findings:
  - statement: PMP70 overexpression rescues PEX2-deficient peroxisome assembly
- id: PMID:9922452
  title: Peroxisome synthesis in the absence of preexisting peroxisomes.
  findings:
  - statement: ABCD3 used as peroxisomal marker to track de novo peroxisome synthesis
- id: PMID:10551832
  title: Homo- and heterodimerization of peroxisomal ATP-binding cassette half-transporters.
  findings:
  - statement: ABCD3 (PMP70) homo- and heterodimerizes with ABCD1 (ALDP) and ABCD2 (ALDRP)
  - statement: Demonstrated by yeast two-hybrid and co-immunoprecipitation
  - statement: C-terminal halves mediate dimerization
- id: PMID:10704444
  title: PEX19 binds multiple peroxisomal membrane proteins, is predominantly cytoplasmic, and is required
    for peroxisome membrane synthesis.
  findings:
  - statement: PEX19 binds ABCD3 and is required for peroxisomal membrane targeting
  - statement: PEX19 is predominantly cytoplasmic
- id: PMID:10777694
  title: Human adrenoleukodystrophy protein and related peroxisomal ABC transporters interact with the
    peroxisomal assembly protein PEX19p.
  findings:
  - statement: ABCD3 interacts with PEX19 for peroxisomal targeting
- id: PMID:11248239
  title: Characterization and functional analysis of the nucleotide binding fold in human peroxisomal
    ATP binding cassette transporters.
  findings:
  - statement: PMP70 NBF binds ATP with KM of 8.2 uM
  - statement: ATP-specific, no GTPase activity
  - statement: G478R mutation decreases ATP binding; S572I decreases ATPase activity
  - statement: NBF mutations do not affect dimerization
- id: PMID:11453642
  title: Targeting elements in the amino-terminal part direct the human 70-kDa peroxisomal integral membrane
    protein (PMP70) to peroxisomes.
  findings:
  - statement: N-terminal targeting elements required for peroxisomal localization
- id: PMID:11590176
  title: Two different targeting signals direct human peroxisomal membrane protein 22 to peroxisomes.
  findings: []
- id: PMID:11883941
  title: Two splice variants of human PEX19 exhibit distinct functions in peroxisomal assembly.
  findings: []
- id: PMID:14709540
  title: PEX19 is a predominantly cytosolic chaperone and import receptor for class 1 peroxisomal membrane
    proteins.
  findings:
  - statement: ABCD3 is a class 1 PMP that uses PEX19 as chaperone/import receptor
- id: PMID:16344115
  title: Role of Pex19p in the targeting of PMP70 to peroxisome.
  findings:
  - statement: PEX19 N-terminal region interacts with ABCD3 N-terminus (aa 1-61)
  - statement: Required for peroxisomal targeting
- id: PMID:17542813
  title: 'Adrenoleukodystrophy: subcellular localization and degradation of adrenoleukodystrophy protein
    (ALDP/ABCD1) with naturally occurring missense mutations.'
  findings:
  - statement: ABCD3 (PMP70) used as peroxisomal marker; confirmed peroxisomal localization
- id: PMID:17609205
  title: 'Live cell FRET microscopy: homo- and heterodimerization of two human peroxisomal ABC transporters,
    the adrenoleukodystrophy protein (ALDP, ABCD1) and PMP70 (ABCD3).'
  findings:
  - statement: ABCD3 forms homodimers in living cells (FRET microscopy)
  - statement: Also forms ABCD1/ABCD3 heterodimers, but ABCD1 homodimers predominate
  - statement: C-terminal 87 amino acids harbor the key dimerization domain
- id: PMID:17761678
  title: Hydrophobic regions adjacent to transmembrane domains 1 and 5 are important for the targeting
    of the 70-kDa peroxisomal membrane protein.
  findings:
  - statement: PMP70 has two distinct peroxisomal targeting signals
  - statement: Hydrophobic regions adjacent to TMD1 and TMD5 are critical
  - statement: L21Q/L22Q/L23Q, I70N/L71Q, I307A/L308A mutations abolish targeting
- id: PMID:19479899
  title: Pex3p-dependent peroxisomal biogenesis initiates in the endoplasmic reticulum of human fibroblasts.
  findings:
  - statement: ABCD3 used as peroxisomal membrane marker
- id: PMID:19946888
  title: Defining the membrane proteome of NK cells.
  findings:
  - statement: ABCD3 identified in NK cell membrane proteome
- id: PMID:20007743
  title: Multiple organelle-targeting signals in the N-terminal portion of peroxisomal membrane protein
    PMP70.
  findings:
  - statement: N-terminal 80aa segment alone targets to outer mitochondrial membrane
  - statement: TM1 segment alone targets to ER
  - statement: Full N80-TM1-TM2 region targets exclusively to peroxisomes
  - statement: N80 segment suppresses ER-targeting function of TM1
- id: PMID:21102411
  title: Structural basis for docking of peroxisomal membrane protein carrier Pex19p onto its receptor
    Pex3p.
  findings:
  - statement: PEX19/PEX3 docking structure relevant to ABCD3 import pathway
- id: PMID:24333844
  title: A role for the human peroxisomal half-transporter ABCD3 in the oxidation of dicarboxylic acids.
  findings:
  - statement: Each peroxisomal half-transporter can function as homodimer
  - statement: ABCD3 preferentially transports hydrophilic substrates including long-chain unsaturated,
      branched-chain, and dicarboxylic fatty acids
  - statement: Substrate specificities of ABCD1, ABCD2, and ABCD3 are overlapping but distinct
  - statement: All substrates transported as CoA esters
  - statement: ABCD3 has a specific role in dicarboxylic acid oxidation
- id: PMID:25168382
  title: A novel bile acid biosynthesis defect due to a deficiency of peroxisomal ABCD3.
  findings:
  - statement: First ABCD3-deficient patient identified with CBAS5
  - statement: Accumulation of C27-bile acid intermediates in plasma
  - statement: Normal C26:0 beta-oxidation but reduced pristanic acid beta-oxidation
  - statement: Abcd3 KO mice accumulate phytanic acid and C27-bile acid intermediates
  - statement: ABCD3 transports branched-chain fatty acids and C27 bile acids into peroxisomes
  - statement: Critical step in bile acid biosynthesis
- id: PMID:29397936
  title: Characterization of human ATP-binding cassette protein subfamily D reconstituted into proteoliposomes.
  findings:
  - statement: ABCD3 displays stable ATPase activity inhibited by AlF3
  - statement: ABCD3 possesses acyl-CoA thioesterase activity equal to ABCD1/2/4
  - statement: Reconstituted in proteoliposomes for functional characterization
- id: PMID:34564857
  title: The peroxisomal transporter ABCD3 plays a major role in hepatic dicarboxylic fatty acid metabolism
    and lipid homeostasis.
  findings:
  - statement: Abcd3 KO mice show increased hepatic long-chain DCAs (C14-C18)
  - statement: Elevated urinary medium-chain DCAs
  - statement: Hepatomegaly, lipodystrophic phenotype
  - statement: Elevated C27 bile acid precursors DHCA and THCA
  - statement: Deficient ketone body production during fasting
  - statement: Enhanced cholesterol synthesis with decreased de novo lipogenesis
- id: PMID:39223112
  title: Structural insights into human ABCD3-mediated peroxisomal acyl-CoA translocation.
  findings:
  - statement: Cryo-EM structures of ABCD3 bound to phytanoyl-CoA (2.9 A) and ATP (3.2 A)
  - statement: Inward-facing and outward-facing conformational states captured
  - statement: Two phytanoyl-CoA molecules bind individually to each TMD
  - statement: DHCA-CoA and THCA-CoA are ABCD3-specific substrates
  - statement: ATP binding causes scissor-like movement expanding translocation cavity
  - statement: PDB codes 8Z0F and 8Z9X
- id: PMID:40501884
  title: Molecular mechanism of substrate transport by human peroxisomal ABCD3.
  findings:
  - statement: Cryo-EM structures of full-length ABCD3 apo (3.33 A) and phytanoyl-CoA-bound (3.13 A)
  - statement: Both inward-facing conformations as homodimer
  - statement: Substrate binding induces 5-fold increase in ATPase activity
  - statement: Substrate binding reduces NBD separation from 38.18 to 34.28 A
  - statement: Proposed transport cycle with substrate-induced NBD closure
- id: Reactome:R-HSA-382575
  title: ABCD1-3 dimers transfer LCFAs from cytosol to peroxisomal matrix
  findings: []
- id: Reactome:R-HSA-382613
  title: PEX-19 docks ABCD1/D2/D3 to peroximal membrane
  findings: []
- id: Reactome:R-HSA-9603775
  title: PEX3:PEX19:class I PMP dissociates
  findings: []
- id: Reactome:R-HSA-9603784
  title: PEX19:class I PMP binds PEX3
  findings: []
- id: Reactome:R-HSA-9603804
  title: PEX19 binds class I peroxisomal membrane proteins
  findings: []
core_functions:
- molecular_function:
    id: GO:0042626
    label: ATPase-coupled transmembrane transporter activity
  description: 'ABCD3 is a peroxisomal ABC half-transporter that homodimerizes to form an active ATP-dependent
    transporter. It catalyzes ATP-driven import of fatty acid substrates (as CoA esters) from the cytosol
    into the peroxisomal lumen. Cryo-EM structures reveal an alternating-access mechanism: substrate binding
    to the inward-open state promotes NBD dimerization, ATP binding drives transition to outward-open
    state for substrate release, and ATP hydrolysis resets the transporter [PMID:39223112, PMID:40501884].'
  directly_involved_in:
  - id: GO:0015910
    label: long-chain fatty acid import into peroxisome
  - id: GO:0006635
    label: fatty acid beta-oxidation
  locations:
  - id: GO:0005778
    label: peroxisomal membrane
  supported_by:
  - reference_id: PMID:29397936
    supporting_text: ABCD1-4 displayed stable ATPase activity, which was inhibited by AlF3
  - reference_id: PMID:39223112
    supporting_text: Upon ATP binding, ABCD3 exhibits a conformation that is open towards the peroxisomal
      matrix, leaving two extra densities corresponding to two CoA molecules deeply embedded in the translocation
      cavity
  - reference_id: PMID:40501884
    supporting_text: Structural comparison of the apo and substrate bound states demonstrate that the substrate
      interaction brings nucleotide-binding domains closer, providing a mechanistic basis of substrate
      induced ATPase activity
- molecular_function:
    id: GO:0005324
    label: long-chain fatty acid transmembrane transporter activity
  description: ABCD3 has broad substrate specificity among the peroxisomal ABC transporters, preferentially
    importing hydrophilic fatty acid substrates including long-chain unsaturated fatty acids, branched-chain
    fatty acids (pristanic acid), dicarboxylic acids (C14-C18), and bile acid CoA-ester intermediates
    (DHCA-CoA, THCA-CoA). This contrasts with ABCD1 which preferentially transports the most hydrophobic
    VLCFAs [PMID:24333844].
  directly_involved_in:
  - id: GO:0015910
    label: long-chain fatty acid import into peroxisome
  - id: GO:1903512
    label: phytanic acid metabolic process
  locations:
  - id: GO:0005778
    label: peroxisomal membrane
  supported_by:
  - reference_id: PMID:24333844
    supporting_text: most hydrophilic substrates like long-chain unsaturated-, long branched-chain- and
      long-chain dicarboxylic fatty acids by HsABCD3
- molecular_function:
    id: GO:0042626
    label: ATPase-coupled transmembrane transporter activity
  description: ABCD3 is the peroxisomal transporter responsible for import of C27-bile acid CoA-ester
    intermediates (DHCA-CoA, THCA-CoA) for side-chain shortening to mature C24 bile acids. Loss of ABCD3
    causes CBAS5 with accumulation of bile acid intermediates. Structural studies identify these as ABCD3-specific
    substrates [PMID:25168382, PMID:39223112]. This represents a unique and non-redundant function of
    ABCD3 within the ABCD transporter family.
  directly_involved_in:
  - id: GO:0015721
    label: bile acid and bile salt transport
  - id: GO:0006699
    label: bile acid biosynthetic process
  locations:
  - id: GO:0005778
    label: peroxisomal membrane
  supported_by:
  - reference_id: PMID:25168382
    supporting_text: ABCD3 is involved in transport of branched-chain fatty acids and C27 bile acids into
      the peroxisome and that this is a crucial step in bile acid biosynthesis
- molecular_function:
    id: GO:0047617
    label: fatty acyl-CoA hydrolase activity
  description: ABCD3 possesses intrinsic thioesterase activity that cleaves fatty acyl-CoAs into free
    fatty acids and CoA. This may be mechanistically coupled to the transport process, with CoA hydrolysis
    occurring during or after substrate translocation [PMID:29397936]. The cryo-EM studies suggest substrates
    may be released either intact or after hydrolysis [PMID:40501884].
  locations:
  - id: GO:0005778
    label: peroxisomal membrane
  supported_by:
  - reference_id: PMID:29397936
    supporting_text: ABCD1-4 were found to possess an equal levels of acyl-CoA thioesterase activity
suggested_questions:
- question: Does ABCD3 transport bile acid CoA-esters as intact molecules or does it hydrolyze the CoA
    moiety during translocation? The cryo-EM structures show substrate bound as intact CoA-ester, but
    thioesterase activity has been demonstrated. What is the physiological transport form?
- question: What is the functional significance of ABCD3 heterodimers with ABCD1 or ABCD2? Do heterodimers
    have different substrate preferences than homodimers?
- question: The Abcd3 KO mice show a lipodystrophic phenotype with altered cholesterol synthesis and decreased
    lipogenesis. Are these direct consequences of impaired peroxisomal import or secondary metabolic adaptations?
suggested_experiments:
- description: In vitro reconstituted transport assays using ABCD3 proteoliposomes with radiolabeled bile
    acid CoA-esters (DHCA-CoA, THCA-CoA) to directly demonstrate ATP-dependent transport of these specific
    substrates and determine whether they are transported intact or hydrolyzed during translocation.
- description: Cryo-EM structures of ABCD3 bound to bile acid CoA-ester substrates to complement the existing
    phytanoyl-CoA-bound structures and reveal any substrate-specific binding modes.
- description: Functional characterization of ABCD3/ABCD1 and ABCD3/ABCD2 heterodimers reconstituted in
    proteoliposomes to determine substrate specificity and transport rates compared to homodimers.

ABCD3

Gene Description

Existing Annotations Review

Core Functions

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Research Report: Functional Annotation of Human ABCD3 / PMP70 (UniProt P28288)

0) Target verification (critical disambiguation)

1) Key concepts and definitions (current understanding)

1.1 Peroxisomal ABCD transporters and “half-transporter” definition

1.2 What ABCD3 does (core definition)

1.3 Mechanistic uncertainty: hydrolysis during transport

2) Molecular function: substrates, ATPase activity, and transport mechanism

2.1 Best-supported transported substrates (substrate specificity)

2.2 2024 structural breakthrough (cryo-EM with substrate)

2.3 Quantitative enzymology (ATPase kinetics)

3) Biological processes and pathways involving ABCD3

3.1 Peroxisomal β-oxidation and metabolic crosstalk

3.2 Dicarboxylic fatty acid (DCA) metabolism (ω-oxidation products)

3.3 Bile-acid biosynthesis (C27-to-C24 side-chain shortening)

3.4 Ether lipid / plasmalogen synthesis (2023 mechanistic link)

4) Subcellular localization, topology, oligomerization, and interaction partners

4.1 Localization and topology

4.2 Oligomeric state: dimers within tetrameric assemblies

4.3 Targeting/biogenesis determinants and peroxisome insertion machinery

4.4 Interaction partners (functional context)

5) Regulation (expression control and modulation)

6) Disease associations and real-world implementations

6.1 Mendelian disease: Congenital bile acid synthesis defect 5 (CBAS5) / ABCD3 deficiency

6.2 Cancer/prognosis associations (expression-based, not causal loss-of-function)

7) Recent developments (prioritizing 2023–2024)

8) Current applications and implementations

9) Statistics and quantitative data (from recent and authoritative studies)

10) Evidence-grounded synthesis (expert-style interpretation)

References (URLs and publication dates as available in retrieved evidence)

Citations

📚 Additional Documentation

Notes

ABCD3 (PMP70) Research Notes

Gene Overview

Key Literature Findings

Substrate Specificity

Bile Acid Transport - Critical Evidence

Dicarboxylic Acid Transport

ATPase and Thioesterase Activities

Cryo-EM Structural Studies

Direct Evidence for ATP-dependent Bile Acid Transport

Dimerization and Interactions

Peroxisome Organization

Key Questions for Review

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