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.
| 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 |
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Download this section (compressed HTML)Q: 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?
Q: What is the functional significance of ABCD3 heterodimers with ABCD1 or ABCD2? Do heterodimers have different substrate preferences than homodimers?
Q: 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?
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.
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