ISCA1 is a mitochondrial matrix A-type iron-sulfur (Fe-S) cluster assembly protein that functions late in the ISC biogenesis pathway, specifically in the maturation of [4Fe-4S] cluster-containing proteins. ISCA1 forms a heterodimeric complex with ISCA2 that acts as an "assembler" of [4Fe-4S] clusters by receiving two [2Fe-2S] clusters from GLRX5 and catalyzing their reductive fusion into a single [4Fe-4S] cluster. This reaction requires the additional factor IBA57 and electrons from the mitochondrial ferredoxin FDX2 and its reductase FDXR. The assembled [4Fe-4S] clusters are then transferred to target apoproteins, with downstream factors NFU1 and BOLA3 mediating insertion for certain targets including lipoic acid synthase (LIAS) and respiratory complex I subunits. ISCA1 is essential for [4Fe-4S] protein maturation but dispensable for [2Fe-2S] proteins. Pathogenic variants cause Multiple Mitochondrial Dysfunctions Syndrome 5 (MMDS5), characterized by infantile-onset leukodystrophy, lactic acidosis, and combined OXPHOS deficiencies.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | REMOVE | Summary: IBA annotation based on phylogenetic inference. While bacterial A-type ISC proteins (IscA) function in the cytoplasm, human ISCA1 is a mitochondrial matrix protein (PMID:22323289). ISCA1 contains a mitochondrial targeting sequence (residues 1-12) and has been experimentally localized to mitochondria. This cytoplasm annotation likely reflects the cytoplasmic function of bacterial orthologs rather than human ISCA1. Reason: Sheftel et al. (PMID:22323289) demonstrated that ISCA1 localizes to mitochondria, not cytoplasm: "ISCA1, ISCA2, and IBA57 are localized to mitochondria". The UniProt entry also indicates mitochondrial localization. While bacterial IscA orthologs function in the cytoplasm, human ISCA1 is a mitochondrial protein. There is no evidence for cytoplasmic ISCA1 function; the authors explicitly state "We further provide evidence against a localization and direct Fe/S protein maturation function of ISCA1 and ISCA2 in the cytosol." Supporting Evidence: PMID:22323289 We further provide evidence against a localization and direct Fe/S protein maturation function of ISCA1 and ISCA2 in the cytosol. file:human/ISCA1/ISCA1-deep-research-falcon.md model: Edison Scientific Literature |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for mitochondrial localization is well supported by experimental evidence. ISCA1 is a mitochondrial matrix protein with a cleavable N-terminal transit peptide (PMID:22323289, PMID:25347204). Reason: Mitochondrial localization of ISCA1 is extensively documented. Sheftel et al. (PMID:22323289) demonstrated mitochondrial localization and showed that depletion causes mitochondrial ultrastructural abnormalities. The IBA annotation is phylogenetically sound and consistent with all experimental evidence. Supporting Evidence: PMID:22323289 ISCA1, ISCA2, and IBA57 are localized to mitochondria |
| GO:0016226 iron-sulfur cluster assembly | IBA GO_REF:0000033 | MODIFY | Summary: ISCA1 is involved in iron-sulfur cluster assembly, specifically in the late-stage maturation of [4Fe-4S] clusters. However, the more specific term GO:0044572 ([4Fe-4S] cluster assembly) better captures ISCA1's function. Reason: While this term is not incorrect, ISCA1 specifically functions in [4Fe-4S] cluster assembly rather than general Fe-S cluster assembly. Sheftel et al. (PMID:22323289) showed that ISCA1 depletion affects [4Fe-4S] proteins (aconitase, complex I, LIAS) but not [2Fe-2S] proteins (ferrochelatase). The more specific term GO:0044572 ([4Fe-4S] cluster assembly) is more appropriate. Proposed replacements: [4Fe-4S] cluster assembly Supporting Evidence: PMID:22323289 In contrast, the mitochondrial [2Fe-2S] enzyme ferrochelatase and cellular heme content were unaffected. |
| GO:0051604 protein maturation | IBA GO_REF:0000033 | ACCEPT | Summary: ISCA1 is involved in protein maturation, specifically the maturation of [4Fe-4S] proteins. This annotation is correct but very general; it could be more specific. Reason: ISCA1 functions in the maturation of [4Fe-4S] proteins by delivering assembled [4Fe-4S] clusters to target apoproteins. The term "protein maturation" is appropriate as a high-level description. PMID:22323289 demonstrates that ISCA1 is "specifically involved in the maturation of mitochondrial [4Fe-4S] proteins." Supporting Evidence: PMID:22323289 ISCA1, ISCA2, and IBA57 are specifically involved in the maturation of mitochondrial [4Fe-4S] proteins functioning late in the ISC assembly pathway. |
| GO:0051537 2 iron, 2 sulfur cluster binding | IBA GO_REF:0000033 | ACCEPT | Summary: ISCA1 can bind [2Fe-2S] clusters as intermediates during [4Fe-4S] cluster assembly. Biochemical reconstitution shows that ISCA1/ISCA2 heterodimer receives [2Fe-2S] clusters from GLRX5 before reductive fusion to form [4Fe-4S] (PMID:25347204). Reason: Brancaccio et al. (PMID:25347204) demonstrated that ISCA1 binds [2Fe-2S] clusters during the [4Fe-4S] assembly process. The [2Fe-2S] binding is transient but essential for the conversion to [4Fe-4S]. Supporting Evidence: PMID:25347204 two molecules of [2Fe-2S](2+) GRX5 donate their cluster to a heterodimeric ISCA1/ISCA2 complex. |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: IEA annotation based on UniProt subcellular location mapping. This is consistent with experimental evidence. Reason: The IEA annotation is consistent with multiple experimental studies confirming mitochondrial localization of ISCA1. UniProt correctly annotates ISCA1 as mitochondrial based on experimental literature. Supporting Evidence: PMID:22323289 ISCA1, ISCA2, and IBA57 are localized to mitochondria |
| GO:0016226 iron-sulfur cluster assembly | IEA GO_REF:0000002 | MODIFY | Summary: IEA annotation based on InterPro domain mapping. The Fe-S biogenesis domain correctly predicts involvement in Fe-S cluster assembly. Reason: While correct at the general level, ISCA1 specifically functions in [4Fe-4S] cluster assembly, not in [2Fe-2S] assembly. The more specific term GO:0044572 ([4Fe-4S] cluster assembly) would be more accurate. Proposed replacements: [4Fe-4S] cluster assembly Supporting Evidence: PMID:22323289 ISCA1, ISCA2, and IBA57 are specifically involved in the maturation of mitochondrial [4Fe-4S] proteins |
| GO:0046872 metal ion binding | IEA GO_REF:0000043 | ACCEPT | Summary: IEA annotation based on UniProt keyword mapping. ISCA1 binds iron as part of iron-sulfur clusters. This is a very general term. Reason: ISCA1 binds iron cations as part of [2Fe-2S] and [4Fe-4S] cluster binding. UniProt lists iron binding sites at positions 57, 121, and 123. While this term is very general, it is technically correct. Supporting Evidence: PMID:25347204 ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state |
| GO:0051536 iron-sulfur cluster binding | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation combining InterPro and UniProt evidence. ISCA1 binds both [2Fe-2S] and [4Fe-4S] clusters during the assembly process. Reason: ISCA1 binds iron-sulfur clusters as part of its function in [4Fe-4S] cluster assembly. It transiently binds [2Fe-2S] clusters received from GLRX5 and can bind the resulting [4Fe-4S] cluster before transfer to target proteins (PMID:25347204). This general term encompasses both cluster types. Supporting Evidence: PMID:25347204 ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state |
| GO:0005515 protein binding | IPI PMID:25347204 Formation of [4Fe-4S] clusters in the mitochondrial iron-sul... | MODIFY | Summary: IPI annotation documenting ISCA1-ISCA2 interaction. The ISCA1-ISCA2 heterodimer is the functional unit for [4Fe-4S] cluster assembly. Reason: While the protein-protein interaction is real, "protein binding" is uninformative. The ISCA1-ISCA2 interaction is central to the protein's core molecular function in [4Fe-4S] cluster assembly. A more specific MF term such as GO:0140132 (iron-sulfur cluster chaperone activity) would better capture ISCA1's function of binding Fe-S clusters and delivering them to acceptor molecules. Proposed replacements: iron-sulfur cluster chaperone activity Supporting Evidence: PMID:25347204 This complex acts as an "assembler" of [4Fe-4S] clusters; i.e., the two GRX5-donated [2Fe-2S](2+) clusters generate a [4Fe-4S](2+) cluster. |
| GO:0005515 protein binding | IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling... | MARK AS OVER ANNOTATED | Summary: IPI annotation from BioPlex high-throughput interactome study. Documents ISCA1-ISCA2 interaction. Reason: This is a duplicate protein binding annotation from a high-throughput study. While the ISCA1-ISCA2 interaction is well-established and functionally important, "protein binding" does not add informative value. The interaction is already documented via PMID:25347204 and the protein's membership in the mitochondrial [4Fe-4S] assembly complex (GO:0120510). Supporting Evidence: PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome |
| GO:0005515 protein binding | IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func... | MARK AS OVER ANNOTATED | Summary: IPI annotation from multimodal cell maps study documenting protein interactions. Reason: Another high-throughput interaction study documenting ISCA1-ISCA2 binding. While confirming the interaction, "protein binding" is uninformative for understanding ISCA1's molecular function. The key interaction with ISCA2 is better captured by the complex membership annotation (GO:0120510). Supporting Evidence: PMID:40205054 Multimodal cell maps as a foundation for structural and functional genomics |
| GO:0005739 mitochondrion | IDA PMID:22323289 The human mitochondrial ISCA1, ISCA2, and IBA57 proteins are... | ACCEPT | Summary: IDA annotation from the key study establishing ISCA1's mitochondrial localization and function. Reason: Sheftel et al. (PMID:22323289) directly demonstrated mitochondrial localization of ISCA1 using multiple approaches. This is the primary experimental evidence for ISCA1's subcellular localization. Supporting Evidence: PMID:22323289 ISCA1, ISCA2, and IBA57 are localized to mitochondria |
| GO:0051604 protein maturation | IDA PMID:25347204 Formation of [4Fe-4S] clusters in the mitochondrial iron-sul... | ACCEPT | Summary: IDA annotation for involvement in protein maturation based on biochemical reconstitution showing ISCA1/ISCA2 function in [4Fe-4S] cluster assembly. Reason: Brancaccio et al. (PMID:25347204) demonstrated that the ISCA1/ISCA2 complex assembles [4Fe-4S] clusters from [2Fe-2S] donors, which is essential for maturation of [4Fe-4S] proteins. The term captures ISCA1's role in protein maturation at a general level. Supporting Evidence: PMID:25347204 heterodimeric complex is the functional unit in mitochondria receiving [2Fe-2S] clusters from hGRX5 and assembling [4Fe-4S] clusters before their transfer to the final target apo proteins. |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | ACCEPT | Summary: HTP annotation from high-confidence mitochondrial proteome study confirming ISCA1 as a mitochondrial protein. Reason: This high-throughput proteomics study (MitoCoP) confirms ISCA1 is a mitochondrial protein, consistent with targeted experimental studies. Supporting Evidence: PMID:34800366 We classified >8,000 proteins in mitochondrial preparations of human cells and defined a mitochondrial high-confidence proteome of >1,100 proteins (MitoCoP). |
| GO:0120510 mitochondrial [4Fe-4S] assembly complex | IDA PMID:25347204 Formation of [4Fe-4S] clusters in the mitochondrial iron-sul... | ACCEPT | Summary: IDA annotation documenting ISCA1 as part of the mitochondrial [4Fe-4S] assembly complex with ISCA2. Reason: Brancaccio et al. (PMID:25347204) demonstrated that ISCA1 forms a heterodimeric complex with ISCA2 that functions as the [4Fe-4S] cluster assembler. This complex term accurately captures ISCA1's molecular context and function. Supporting Evidence: PMID:25347204 two molecules of [2Fe-2S](2+) GRX5 donate their cluster to a heterodimeric ISCA1/ISCA2 complex. |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-8878815 | ACCEPT | Summary: TAS annotation from Reactome pathway "Formation of 4Fe-4S cluster on ISCA1:ISCA2". Specifies mitochondrial matrix localization. Reason: ISCA1 functions in the mitochondrial matrix, as established by both experimental studies and pathway databases. The mitochondrial matrix is the more specific localization compared to general mitochondrion. Supporting Evidence: PMID:22323289 ISCA1, ISCA2, and IBA57 are localized to mitochondria |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-9854984 | ACCEPT | Summary: TAS annotation from Reactome pathway "Transfer of Fe-S clusters to SDHB". Documents ISCA1's role in delivering [4Fe-4S] clusters to target proteins. Reason: This annotation documents the downstream function of ISCA1 in delivering [4Fe-4S] clusters to target proteins like SDHB. The mitochondrial matrix localization is correct. Supporting Evidence: PMID:25347204 heterodimeric complex is the functional unit in mitochondria receiving [2Fe-2S] clusters from hGRX5 and assembling [4Fe-4S] clusters before their transfer to the final target apo proteins. |
| GO:0044572 [4Fe-4S] cluster assembly | IDA PMID:22323289 The human mitochondrial ISCA1, ISCA2, and IBA57 proteins are... | NEW | Summary: ISCA1 specifically functions in [4Fe-4S] cluster assembly, not general Fe-S cluster assembly. This is the more specific BP term for ISCA1's function. Reason: Sheftel et al. (PMID:22323289) demonstrated that ISCA1 depletion specifically affects [4Fe-4S] proteins but not [2Fe-2S] proteins. This term more accurately captures ISCA1's specific function in the late-stage ISC assembly pathway. Supporting Evidence: PMID:22323289 In contrast, the mitochondrial [2Fe-2S] enzyme ferrochelatase and cellular heme content were unaffected. PMID:25347204 This complex acts as an "assembler" of [4Fe-4S] clusters; i.e., the two GRX5-donated [2Fe-2S](2+) clusters generate a [4Fe-4S](2+) cluster. |
| GO:0140132 iron-sulfur cluster chaperone activity | IDA PMID:25347204 Formation of [4Fe-4S] clusters in the mitochondrial iron-sul... | NEW | Summary: ISCA1 functions as an Fe-S cluster chaperone, binding [2Fe-2S] clusters from GLRX5, converting them to [4Fe-4S], and delivering them to target proteins. Reason: This MF term accurately describes ISCA1's molecular function of "binding to an iron-sulfur cluster and delivering it to an acceptor molecule." Brancaccio et al. demonstrated this chaperone function biochemically. Supporting Evidence: PMID:25347204 heterodimeric complex is the functional unit in mitochondria receiving [2Fe-2S] clusters from hGRX5 and assembling [4Fe-4S] clusters before their transfer to the final target apo proteins. |
| GO:0051539 4 iron, 4 sulfur cluster binding | IDA PMID:25347204 Formation of [4Fe-4S] clusters in the mitochondrial iron-sul... | NEW | Summary: The ISCA1/ISCA2 complex binds [4Fe-4S] clusters after assembly and before transfer to target proteins. Reason: Brancaccio et al. (PMID:25347204) showed that after reductive fusion of two [2Fe-2S] clusters, the ISCA1/ISCA2 heterodimer holds a [4Fe-4S] cluster before transfer to target proteins. Both [2Fe-2S] binding (existing annotation) and [4Fe-4S] binding should be annotated. Supporting Evidence: PMID:25347204 ISCA2 binds either [2Fe-2S] or [4Fe-4S] cluster in a dimeric state |
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Download this section (compressed HTML)Experiment: Structural characterization of the human ISCA1/ISCA2/IBA57 complex with bound Fe-S clusters to understand the molecular mechanism of [2Fe-2S] to [4Fe-4S] conversion.
Experiment: Identification of the complete set of [4Fe-4S] target proteins that depend on ISCA1/ISCA2 for cluster acquisition versus those using alternative delivery pathways.
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