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 | MODIFY | 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: Correct but general for ABCD3. Its ATPase-coupled transport substrate is the acyl-CoA thioester (CoA moieties sit in the translocation cavity of purified human ABCD3), so the specific child term ABC-type fatty-acyl-CoA transporter activity (GO:0015607) describes the activity, as it does for the paralog ABCD1. The general term remains right for the family node itself. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN008319914 SUPPORTS TRANSFER ABCD-family node whose WITH/FROM includes human ABCD1, ABCD2, ABCD3 (the target itself) and ABCD4 and yeast PXA1/PXA2. The family includes the lysosomal cobalamin transporter ABCD4, so the general ATPase-coupled transporter term is the appropriate node-level assertion; the transfer is sound and the MODIFY only sharpens the term for ABCD3. Proposed replacements: ABC-type fatty-acyl-CoA transporter activity Supporting Evidence: PMID:39223112 extra densities corresponding to two CoA molecules deeply embedded in the translocation cavity 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]. The 2024 cryo-EM study cites this ABCD3 specificity for DHCA/THCA CoA esters as background [PMID:39223112], but its structures are phytanoyl-CoA- and ATP-bound, not bile acid-bound. Reason: Well-supported by patient genetics and knockout mice. The ABCD3 specificity for DHCA-CoA and THCA-CoA rests on these loss-of-function data, not on cryo-EM ligand structures. 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 | MODIFY | Summary: InterPro-based annotation. Consistent with IDA evidence from proteoliposome studies [PMID:29397936]. Reason: Correct but general; the specific acyl-CoA transporter child term GO:0015607 describes ABCD3's activity (see the IDA row for this term). Proposed replacements: ABC-type fatty-acyl-CoA transporter activity |
| 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 and Abcd3-/- mice [PMID:25168382]; the cryo-EM study [PMID:39223112] restates this substrate specificity as background but resolved only phytanoyl-CoA- and ATP-bound structures. Reason: Core function. In vivo loss-of-function in patient and mouse confirms the bile acid transport role. The ABCD3 structures reported to date are phytanoyl-CoA- and ATP-bound [PMID:39223112] and apo and phytanoyl-CoA-bound [PMID:40501884], with no bile acid CoA-ester-bound state; the full text of PMID:39223112 also reports no direct DHCA-CoA/THCA-CoA transport assay. 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... | MODIFY | 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, directly demonstrated in a reconstituted system with structural validation of the transport mechanism. Purified human ABCD3 binds phytanoyl-CoA in its translocation cavity and, on ATP binding, opens to the peroxisomal matrix with the CoA moieties embedded, so its transport substrate is the acyl-CoA thioester and the specific child term GO:0015607 applies. Proposed replacements: ABC-type fatty-acyl-CoA transporter activity 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 PMID:39223112 extra densities corresponding to two CoA molecules deeply embedded in the translocation cavity |
| 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. Supporting Evidence: PMID:9922452 PMP70, an integral membrane protein of the peroxisome |
| 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. Supporting Evidence: PMID:10704444 The first 124 amino acids of PMP70 were sufficient to direct it into peroxisomes |
| 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]. The cryo-EM study of ABCD3 [PMID:39223112] lists DHCA/THCA CoA esters among ABCD3-specific substrates in its introduction, citing PMID:25168382, but its structures and ATPase assays used phytanoyl-CoA and straight-chain acyl-CoAs, not bile acid CoA-esters. 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 and KO mice; direct in vitro transport of bile acid CoA-esters remains to be shown (see the reconstituted DHCA-CoA/THCA-CoA transport assay in suggested_experiments). The transported species is the CoA thioester of a C27 bile acid intermediate, whereas GO:0015125 is defined over bile acids; no GO term for bile acid-CoA transmembrane transport was found, so GO:0015125 is the closest available fit. 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 a different substrate (phytanoyl-CoA) bound as an 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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