{"gene":"LYRM4","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2005,"finding":"Isd11 (LYRM4 ortholog in yeast) forms a stable complex with the cysteine desulfurase Nfs1; in the absence of Isd11, Nfs1 is prone to aggregation, and Fe/S cluster assembly on scaffold proteins is abrogated, placing Isd11 at an early step in Fe/S cluster biogenesis.","method":"Genetic depletion, co-immunoprecipitation, enzymatic activity assays (aconitase, succinate dehydrogenase), iron incorporation into Leu1, holoform formation of ferredoxin Yah1","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — two independent labs (Adam et al. and Wiedemann et al.) published simultaneously with multiple orthogonal methods: co-IP, enzymatic assays, iron incorporation, scaffold loading","pmids":["16341090","16341089"],"is_preprint":false},{"year":2005,"finding":"Isd11 is required for formation of an Fe/S cluster on the Isu scaffold proteins and is an indispensable eukaryotic component of the mitochondrial ISC-assembly machinery.","method":"Genetic deletion/depletion in yeast, Fe/S cluster loading assay on Isu scaffold, co-immunoprecipitation with Nfs1","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — independent replication by Wiedemann et al. using deletion genetics and scaffold loading assays","pmids":["16341089"],"is_preprint":false},{"year":2007,"finding":"Human ISD11 interacts with frataxin in mammalian cells; Friedreich's ataxia point mutations I154F and W155R in frataxin reduce the frataxin-ISD11 interaction; ISD11 depletion by siRNA reduces the NFS1/ISCU complex levels and aconitase activity while increasing cellular iron content.","method":"Co-immunoprecipitation, mass spectrometry, siRNA knockdown, aconitase activity assay, immunofluorescence co-localization","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP confirmed interactions, siRNA functional readout, single lab with multiple orthogonal methods","pmids":["17331979"],"is_preprint":false},{"year":2009,"finding":"Human ISD11 localizes to both mitochondria and nucleus; it forms a stable in vivo complex with human cysteine desulfurase ISCS (NFS1); ISD11 knockdown inactivates mitochondrial and cytosolic aconitases, activates IRP1 iron-responsive element-binding activity, increases IRP2 protein levels, and causes abnormal ferric iron accumulations, linking ISD11 to cellular iron homeostasis.","method":"Subcellular fractionation/immunofluorescence, co-immunoprecipitation, RNA interference, aconitase activity assay, IRP activity assay","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization with functional consequence, co-IP, multiple functional readouts; single lab","pmids":["19454487"],"is_preprint":false},{"year":2011,"finding":"Mammalian frataxin interacts with a preformed ISCU/NFS1/ISD11 core complex (not individual components) to form a stable quaternary complex of ~190 kDa; this interaction defines the essential function of frataxin in Fe-S cluster biosynthesis.","method":"Co-immunoprecipitation (in vivo and in vitro), heterologous expression system, size-exclusion chromatography","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — combined in vitro reconstitution and in vivo co-IP with complex isolation; single lab","pmids":["21298097"],"is_preprint":false},{"year":2013,"finding":"A homozygous missense mutation R68L in human LYRM4/ISD11 causes combined OXPHOS deficiency (complexes I, II, III) and impairs Fe/S protein assembly; mutant ISD11 only partially complements yeast ISD11 deletion, and co-expression of mutant ISD11 with NFS1 yields nearly absent l-cysteine desulfurase activity in vitro.","method":"MitoExome sequencing, Sanger sequencing, yeast complementation assay, in vitro cysteine desulfurase activity assay with mutant protein","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro enzymatic assay with mutant protein, yeast complementation, patient biochemical data; multiple orthogonal methods","pmids":["23814038"],"is_preprint":false},{"year":2015,"finding":"Key ISD11 residues in helix 1 (Phe-40), helix 3 (Leu-63, Arg-68, Gln-69, Ile-72, Tyr-76), and C-terminal segment (Leu-81, Glu-84) are critical for interaction with NFS1; mutations at these sites reduce NFS1 stability, cause NFS1 aggregation, deplete ISCU levels, impair Fe/S cluster biosynthesis, reduce ETC complex activity, and diminish mitochondrial respiration. The disease mutation R68L/R68A reduces ISD11-NFS1 complex stability and causes mitochondrial iron accumulation and ROS elevation.","method":"Site-directed mutagenesis, co-immunoprecipitation, NFS1 aggregation assay, aconitase activity, ETC complex activity assays, mitochondrial respiration measurements, iron/ROS detection","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — systematic mutagenesis with multiple functional readouts (co-IP, aggregation, enzyme activity, respiration) in a single rigorous study","pmids":["26342079"],"is_preprint":false},{"year":2017,"finding":"Crystal and EM structures of the human NFS1-ISD11-ACP (SDA) complex reveal that ISD11 subunits form the dimeric core of the complex (not NFS1 as in prokaryotes); the 4'-phosphopantetheine-conjugated acyl group of ACP occupies the hydrophobic core of ISD11, explaining ACP's role in stabilizing ISD11; the architecture creates an incompletely formed substrate channel and solvent-exposed PLP cofactor, explaining why FXN acts as an allosteric activator in eukaryotes.","method":"X-ray crystallography, cryo-EM, enzyme kinetic assays, cell-based complementation studies","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution crystal structure and cryo-EM validated by kinetics and cell-based assays; multiple orthogonal methods in one rigorous study","pmids":["28634302"],"is_preprint":false},{"year":2017,"finding":"When NFS1 and ISD11 are co-expressed in E. coli, the active preparation contains E. coli acyl carrier protein (ACP) in a stoichiometric [Acp]2:[ISD11]2:[NFS1]2 complex; E. coli ACP can substitute for human ACP in supporting Fe/S cluster assembly in vitro.","method":"Recombinant co-expression, mass spectrometry stoichiometry determination, in vitro Fe/S cluster assembly assay","journal":"ACS chemical biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — reconstituted complex with defined stoichiometry and functional in vitro assay; single lab but multiple orthogonal methods","pmids":["28233492"],"is_preprint":false},{"year":2017,"finding":"The first 10 N-terminal amino acids of ISD11, including the conserved LYR motif, are indispensable for NFS1 activity and for forming a stable, active complex with NFS1; N-terminal truncations also disrupt mitochondrial targeting.","method":"In vitro purified protein interaction assays, NFS1 activity assays with N-terminal ISD11 mutants, cell-based subcellular localization studies","journal":"Biochemistry","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — in vitro and in vivo studies with defined N-terminal mutants and functional readouts; single lab","pmids":["28271877"],"is_preprint":false},{"year":2013,"finding":"Isd11 has a profound effect on the oligomeric state of Nfs1: the presence of Isd11 alters the quaternary structure of the eukaryotic cysteine desulfurase complex.","method":"Biochemical characterization of oligomeric state (size-exclusion chromatography / biophysical analysis) with and without Isd11","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single biophysical method, single lab, limited mechanistic follow-up","pmids":["24045011"],"is_preprint":false},{"year":2016,"finding":"Human ISD11 alone exists in solution as an equilibrium of monomeric, dimeric, and tetrameric species; recombinant ISD11 expressed in E. coli co-purifies with bacterial IscS (the prokaryotic NFS1 ortholog) in a weak but specific interaction, indicating conservation of the desulfurase-binding surface.","method":"Analytical ultracentrifugation/gel filtration, co-purification from E. coli, binding specificity analysis","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — co-purification and biophysical characterization; single lab, limited functional follow-up","pmids":["27427956"],"is_preprint":false},{"year":2018,"finding":"Human mitochondrial ACP and ISD11 form a soluble, structured, and stable complex when co-expressed in E. coli; ACP plays a key role in ISD11 folding and stability in vitro; the ACP-ISD11 complex binds NFS1 and modulates its cysteine desulfurase activity.","method":"Recombinant co-expression, co-purification, NFS1 activity assay, structural characterization","journal":"ACS chemical biology","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — reconstituted complex with functional enzyme activity assay; single lab","pmids":["29737835"],"is_preprint":false},{"year":2019,"finding":"Crystal structure of the human mitochondrial ACP-ISD11 heterodimer at 2.0 Å resolution reveals stabilization via ionic interactions, hydrogen bonds, and apolar contacts; the 4'-phosphopantetheine-acyl chain of ACP interacts with specific ISD11 residues, modulating ISD11 foldability; the ACP-ISD11 complex interacts with NFS1 yielding an active enzyme that is further activated by frataxin and ISCU.","method":"X-ray crystallography (2.0 Å), molecular dynamics simulations, NFS1 activity assay, protein-protein interaction assay","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — high-resolution crystal structure with functional enzyme assay and MD validation; single lab but multiple orthogonal methods","pmids":["31664822"],"is_preprint":false},{"year":2010,"finding":"In Trypanosoma brucei, Isd11 localizes to the mitochondrion and is required not only for Fe/S cluster assembly but also for both cytoplasmic and mitochondrial tRNA thiolation, placing Isd11 at the center of sulfur transfer pathways that connect Fe/S metabolism and tRNA modification.","method":"RNA interference (genetic depletion), subcellular fractionation/localization, biochemical tRNA thiolation assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — genetic depletion with functional tRNA thiolation assay in a divergent eukaryote; single lab","pmids":["20442400"],"is_preprint":false},{"year":2025,"finding":"Elevated LYRM4 expression enhances the enzymatic activity of succinate dehydrogenase (SDH), promoting fumarate accumulation in hepatocellular carcinoma cells.","method":"Functional genomics (TUIFGA), SDH enzymatic activity assay, cellular metabolite measurement","journal":"Archives of biochemistry and biophysics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, limited mechanistic follow-up in abstract, no direct biochemical reconstitution described","pmids":["40320061"],"is_preprint":false}],"current_model":"LYRM4/ISD11 is a small LYR-motif protein that forms the dimeric core of the eukaryote-specific NFS1-ISD11-ACP (SDA) cysteine desulfurase complex in mitochondria: ISD11 stabilizes NFS1 against aggregation and, together with acyl carrier protein (ACP) whose phosphopantetheine-acyl chain occupies the hydrophobic core of ISD11, establishes the quaternary architecture required for sulfur mobilization; the SDA complex then recruits ISCU2, frataxin (as an allosteric activator), and ferredoxin to assemble Fe/S clusters, with defined ISD11 residues (including the N-terminal LYR motif and helix-3 residue R68) being critical for NFS1 interaction, complex stability, and downstream Fe/S-dependent respiratory chain function."},"narrative":{"mechanistic_narrative":"LYRM4 (ISD11) is a small LYR-motif mitochondrial protein that functions as an essential eukaryotic component of the cysteine desulfurase machinery that initiates iron-sulfur (Fe/S) cluster biogenesis [PMID:16341090, PMID:16341089]. It forms a stable complex with the cysteine desulfurase NFS1 (Nfs1/ISCS), stabilizing the desulfurase against aggregation and altering its oligomeric state, such that loss of ISD11 abrogates Fe/S cluster loading onto the Isu/ISCU scaffold [PMID:16341090, PMID:16341089, PMID:24045011]. In the assembled NFS1-ISD11-ACP (SDA) complex, ISD11 subunits form the dimeric core of the eukaryotic enzyme, and the 4'-phosphopantetheine-acyl chain of acyl carrier protein (ACP) occupies the hydrophobic core of ISD11, an interaction required for ISD11 folding and stability; this architecture leaves an incompletely formed substrate channel and solvent-exposed PLP cofactor, accounting for frataxin's role as an allosteric activator in eukaryotes [PMID:28634302, PMID:28233492, PMID:31664822]. The SDA complex assembles with ISCU and frataxin into a stable quaternary complex, and ISD11 residues including the N-terminal LYR motif and helix-3 Arg-68 are critical for NFS1 interaction, complex stability, and downstream Fe/S-dependent respiratory chain function [PMID:21298097, PMID:26342079, PMID:28271877]. Through its control of Fe/S cluster assembly, ISD11 governs the activity of aconitases and the electron transport chain and influences cellular iron homeostasis via IRP regulation [PMID:17331979, PMID:19454487]. A homozygous R68L missense mutation in human LYRM4 causes combined OXPHOS deficiency by destabilizing the ISD11-NFS1 complex and abolishing cysteine desulfurase activity [PMID:23814038, PMID:26342079].","teleology":[{"year":2005,"claim":"Established that ISD11 is an indispensable, eukaryote-specific partner of the cysteine desulfurase NFS1/Nfs1 acting at the earliest step of Fe/S cluster biogenesis, answering whether a dedicated factor stabilizes the desulfurase.","evidence":"Genetic depletion in yeast with co-IP, enzymatic activity assays, iron incorporation, and Isu scaffold loading, replicated by two independent labs","pmids":["16341090","16341089"],"confidence":"High","gaps":["Did not define the structural basis of NFS1 stabilization","Stoichiometry and full complex composition not resolved"]},{"year":2007,"claim":"Connected human ISD11 to frataxin and to disease, showing the desulfurase complex is a target of Friedreich's ataxia mutations and a regulator of cellular iron.","evidence":"Co-IP/mass spectrometry, siRNA knockdown, aconitase and iron content assays in mammalian cells","pmids":["17331979"],"confidence":"Medium","gaps":["Whether frataxin binds ISD11 directly or via the core complex unresolved here","Single lab"]},{"year":2009,"claim":"Demonstrated that human ISD11 controls both mitochondrial and cytosolic Fe/S-dependent enzymes and iron-regulatory protein activity, linking it to whole-cell iron homeostasis.","evidence":"Subcellular fractionation, co-IP with NFS1/ISCS, RNAi, aconitase and IRP activity assays","pmids":["19454487"],"confidence":"Medium","gaps":["Reported nuclear localization not mechanistically explained","Single lab"]},{"year":2011,"claim":"Showed frataxin engages a preformed ISCU/NFS1/ISD11 core rather than individual components, defining the quaternary complex frataxin acts upon.","evidence":"In vivo and in vitro co-IP with size-exclusion chromatography of a ~190 kDa complex","pmids":["21298097"],"confidence":"Medium","gaps":["Did not resolve subunit arrangement or stoichiometry","ACP not yet identified as a subunit"]},{"year":2013,"claim":"Identified a disease-causing LYRM4 mutation (R68L) and established ISD11's effect on the oligomeric state of the desulfurase, tying a specific residue to enzyme function and OXPHOS.","evidence":"MitoExome/Sanger sequencing, yeast complementation, in vitro cysteine desulfurase assay with mutant; separate biophysical oligomeric-state analysis","pmids":["23814038","24045011"],"confidence":"High","gaps":["Structural mechanism by which R68L destabilizes the complex not defined at this stage"]},{"year":2015,"claim":"Mapped the ISD11 surface required for NFS1 binding through systematic mutagenesis, defining residues whose loss causes NFS1 aggregation, ISCU depletion, and respiratory failure.","evidence":"Site-directed mutagenesis with co-IP, aggregation assays, ETC complex activity, respiration, and iron/ROS measurements","pmids":["26342079"],"confidence":"High","gaps":["Lacked atomic structure to interpret residue contributions","ACP contribution not yet incorporated"]},{"year":2017,"claim":"Solved the architecture of the SDA complex, revealing ISD11 dimers as the core, ACP's acyl chain buried in ISD11, and the structural basis for frataxin acting as an allosteric activator.","evidence":"X-ray crystallography and cryo-EM with enzyme kinetics and cell-based complementation; recombinant co-expression with defined [ACP]2:[ISD11]2:[NFS1]2 stoichiometry and in vitro Fe/S assays; N-terminal LYR-motif mutagenesis","pmids":["28634302","28233492","28271877"],"confidence":"High","gaps":["Dynamics of substrate channel formation during catalysis not captured","How acyl-chain identity tunes activity not resolved"]},{"year":2018,"claim":"Established ACP as a folding chaperone for ISD11 and confirmed the ACP-ISD11 module binds and modulates NFS1 activity, clarifying why ACP is required for complex stability.","evidence":"Recombinant co-expression, co-purification, structural characterization, and NFS1 activity assays","pmids":["29737835"],"confidence":"Medium","gaps":["Single lab","Physiological acyl-chain occupancy in vivo not quantified"]},{"year":2019,"claim":"Provided a high-resolution ACP-ISD11 heterodimer structure detailing the interface and acyl-chain contacts that modulate ISD11 foldability and enable NFS1 activation by frataxin and ISCU.","evidence":"2.0 Å X-ray crystallography, molecular dynamics, NFS1 activity and interaction assays","pmids":["31664822"],"confidence":"High","gaps":["Conformational changes upon frataxin/ISCU binding not captured in this structure","Single lab"]},{"year":2010,"claim":"Extended ISD11 function beyond Fe/S clusters by showing it is required for cytoplasmic and mitochondrial tRNA thiolation in Trypanosoma brucei, placing it at a sulfur-transfer hub.","evidence":"RNAi depletion, subcellular localization, and tRNA thiolation assays in a divergent eukaryote","pmids":["20442400"],"confidence":"Medium","gaps":["Direct role in human tRNA thiolation not demonstrated","Single lab, divergent organism"]},{"year":2025,"claim":"Linked elevated LYRM4 to altered metabolism in hepatocellular carcinoma via enhanced SDH activity and fumarate accumulation.","evidence":"Functional genomics, SDH activity assay, and metabolite measurement in HCC cells","pmids":["40320061"],"confidence":"Low","gaps":["No direct biochemical reconstitution described","Mechanism connecting LYRM4 to SDH activity not established","Single lab"]},{"year":null,"claim":"How the SDA complex dynamically coordinates frataxin and ISCU recruitment, ferredoxin electron delivery, and sulfur channeling during catalytic Fe/S cluster turnover, and whether human ISD11 directly supports tRNA thiolation, remain open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No catalytic-cycle structure of the full assembly","Human tRNA thiolation role untested","Regulation of LYRM4 expression in disease contexts unclear"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,5,6,13]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,7,12,13]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[3,9,14]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,1,3]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,1]}],"complexes":["NFS1-ISD11-ACP (SDA) cysteine desulfurase complex","ISCU/NFS1/ISD11 core complex"],"partners":["NFS1","NDUFAB1","ISCU","FXN"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9HD34","full_name":"LYR motif-containing protein 4","aliases":[],"length_aa":91,"mass_kda":10.8,"function":"Stabilizing factor, of the core iron-sulfur cluster (ISC) assembly complex, that regulates, in association with NDUFAB1, the stability and the cysteine desulfurase activity of NFS1 and participates in the [2Fe-2S] clusters assembly on the scaffolding protein ISCU (PubMed:17331979, PubMed:31664822). The core iron-sulfur cluster (ISC) assembly complex is involved in the de novo synthesis of a [2Fe-2S] cluster, the first step of the mitochondrial iron-sulfur protein biogenesis. This process is initiated by the cysteine desulfurase complex (NFS1:LYRM4:NDUFAB1) that produces persulfide which is delivered on the scaffold protein ISCU in a FXN-dependent manner. Then this complex is stabilized by FDX2 which provides reducing equivalents to accomplish the [2Fe-2S] cluster assembly. Finally, the [2Fe-2S] cluster is transferred from ISCU to chaperone proteins, including HSCB, HSPA9 and GLRX5 (By similarity). May also participates in the iron-sulfur protein biogenesis in the cytoplasm through its interaction with the cytoplasmic form of NFS1 (PubMed:19454487)","subcellular_location":"Mitochondrion; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9HD34/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/LYRM4","classification":"Common Essential","n_dependent_lines":1187,"n_total_lines":1208,"dependency_fraction":0.9826158940397351},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/LYRM4","total_profiled":1310},"omim":[{"mim_id":"615595","title":"COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 19; COXPD19","url":"https://www.omim.org/entry/615595"},{"mim_id":"614946","title":"COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 14; COXPD14","url":"https://www.omim.org/entry/614946"},{"mim_id":"613311","title":"LYR MOTIF-CONTAINING PROTEIN 4; LYRM4","url":"https://www.omim.org/entry/613311"},{"mim_id":"611592","title":"PHENYLALANYL-tRNA SYNTHETASE 2, MITOCHONDRIAL; FARS2","url":"https://www.omim.org/entry/611592"},{"mim_id":"609060","title":"COMBINED OXIDATIVE PHOSPHORYLATION DEFICIENCY 1; COXPD1","url":"https://www.omim.org/entry/609060"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nuclear bodies","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/LYRM4"},"hgnc":{"alias_symbol":["CGI-203","ISD11"],"prev_symbol":["C6orf149"]},"alphafold":{"accession":"Q9HD34","domains":[{"cath_id":"-","chopping":"10-79","consensus_level":"high","plddt":97.2867,"start":10,"end":79}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9HD34","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9HD34-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9HD34-F1-predicted_aligned_error_v6.png","plddt_mean":93.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LYRM4","jax_strain_url":"https://www.jax.org/strain/search?query=LYRM4"},"sequence":{"accession":"Q9HD34","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9HD34.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9HD34/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9HD34"}},"corpus_meta":[{"pmid":"16341090","id":"PMC_16341090","title":"The Nfs1 interacting protein Isd11 has an essential role in Fe/S cluster biogenesis in mitochondria.","date":"2005","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/16341090","citation_count":190,"is_preprint":false},{"pmid":"21298097","id":"PMC_21298097","title":"Mammalian frataxin: an essential function for cellular viability through an interaction with a preformed ISCU/NFS1/ISD11 iron-sulfur assembly complex.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21298097","citation_count":190,"is_preprint":false},{"pmid":"16341089","id":"PMC_16341089","title":"Essential role of Isd11 in mitochondrial iron-sulfur cluster synthesis on Isu scaffold proteins.","date":"2005","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/16341089","citation_count":183,"is_preprint":false},{"pmid":"28634302","id":"PMC_28634302","title":"Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions.","date":"2017","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/28634302","citation_count":127,"is_preprint":false},{"pmid":"17331979","id":"PMC_17331979","title":"Mitochondrial frataxin interacts with ISD11 of the NFS1/ISCU complex and multiple mitochondrial chaperones.","date":"2007","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/17331979","citation_count":125,"is_preprint":false},{"pmid":"19454487","id":"PMC_19454487","title":"Human ISD11 is essential for both iron-sulfur cluster assembly and maintenance of normal cellular iron homeostasis.","date":"2009","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/19454487","citation_count":119,"is_preprint":false},{"pmid":"23814038","id":"PMC_23814038","title":"Mutations in LYRM4, encoding iron-sulfur cluster biogenesis factor ISD11, cause deficiency of multiple respiratory chain complexes.","date":"2013","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/23814038","citation_count":92,"is_preprint":false},{"pmid":"16648156","id":"PMC_16648156","title":"Evolution of the Isd11-IscS complex reveals a single alpha-proteobacterial endosymbiosis for all eukaryotes.","date":"2006","source":"Molecular biology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/16648156","citation_count":58,"is_preprint":false},{"pmid":"34124036","id":"PMC_34124036","title":"Exosomes Isolated From Bone Marrow Mesenchymal Stem Cells Exert a Protective Effect on Osteoarthritis via lncRNA LYRM4-AS1-GRPR-miR-6515-5p.","date":"2021","source":"Frontiers in cell and developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/34124036","citation_count":45,"is_preprint":false},{"pmid":"28233492","id":"PMC_28233492","title":"Mitochondrial Cysteine Desulfurase and ISD11 Coexpressed in Escherichia coli Yield Complex Containing Acyl Carrier Protein.","date":"2017","source":"ACS chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/28233492","citation_count":32,"is_preprint":false},{"pmid":"20442400","id":"PMC_20442400","title":"The Fe/S cluster assembly protein Isd11 is essential for tRNA thiolation in Trypanosoma brucei.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20442400","citation_count":29,"is_preprint":false},{"pmid":"26342079","id":"PMC_26342079","title":"Mapping Key Residues of ISD11 Critical for NFS1-ISD11 Subcomplex Stability: IMPLICATIONS IN THE DEVELOPMENT OF MITOCHONDRIAL DISORDER, COXPD19.","date":"2015","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26342079","citation_count":26,"is_preprint":false},{"pmid":"29737835","id":"PMC_29737835","title":"Rescuing the Rescuer: On the Protein Complex between the Human Mitochondrial Acyl Carrier Protein and ISD11.","date":"2018","source":"ACS chemical 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communications","url":"https://pubmed.ncbi.nlm.nih.gov/24045011","citation_count":15,"is_preprint":false},{"pmid":"31497476","id":"PMC_31497476","title":"Iron-sulfur cluster ISD11 deficiency (LYRM4 gene) presenting as cardiorespiratory arrest and 3-methylglutaconic aciduria.","date":"2019","source":"JIMD reports","url":"https://pubmed.ncbi.nlm.nih.gov/31497476","citation_count":10,"is_preprint":false},{"pmid":"27427956","id":"PMC_27427956","title":"The Eukaryotic-Specific ISD11 Is a Complex-Orphan Protein with Ability to Bind the Prokaryotic IscS.","date":"2016","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/27427956","citation_count":8,"is_preprint":false},{"pmid":"40320061","id":"PMC_40320061","title":"Integrated functional genomics-identified LYRM4 promotes fumarate accumulation and hepatocellular carcinoma progression.","date":"2025","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/40320061","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10716,"output_tokens":3919,"usd":0.045466,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11703,"output_tokens":3643,"usd":0.074795,"stage2_stop_reason":"end_turn"},"total_usd":0.120261,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2005,\n      \"finding\": \"Isd11 (LYRM4 ortholog in yeast) forms a stable complex with the cysteine desulfurase Nfs1; in the absence of Isd11, Nfs1 is prone to aggregation, and Fe/S cluster assembly on scaffold proteins is abrogated, placing Isd11 at an early step in Fe/S cluster biogenesis.\",\n      \"method\": \"Genetic depletion, co-immunoprecipitation, enzymatic activity assays (aconitase, succinate dehydrogenase), iron incorporation into Leu1, holoform formation of ferredoxin Yah1\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — two independent labs (Adam et al. and Wiedemann et al.) published simultaneously with multiple orthogonal methods: co-IP, enzymatic assays, iron incorporation, scaffold loading\",\n      \"pmids\": [\"16341090\", \"16341089\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Isd11 is required for formation of an Fe/S cluster on the Isu scaffold proteins and is an indispensable eukaryotic component of the mitochondrial ISC-assembly machinery.\",\n      \"method\": \"Genetic deletion/depletion in yeast, Fe/S cluster loading assay on Isu scaffold, co-immunoprecipitation with Nfs1\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — independent replication by Wiedemann et al. using deletion genetics and scaffold loading assays\",\n      \"pmids\": [\"16341089\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Human ISD11 interacts with frataxin in mammalian cells; Friedreich's ataxia point mutations I154F and W155R in frataxin reduce the frataxin-ISD11 interaction; ISD11 depletion by siRNA reduces the NFS1/ISCU complex levels and aconitase activity while increasing cellular iron content.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, siRNA knockdown, aconitase activity assay, immunofluorescence co-localization\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP confirmed interactions, siRNA functional readout, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"17331979\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Human ISD11 localizes to both mitochondria and nucleus; it forms a stable in vivo complex with human cysteine desulfurase ISCS (NFS1); ISD11 knockdown inactivates mitochondrial and cytosolic aconitases, activates IRP1 iron-responsive element-binding activity, increases IRP2 protein levels, and causes abnormal ferric iron accumulations, linking ISD11 to cellular iron homeostasis.\",\n      \"method\": \"Subcellular fractionation/immunofluorescence, co-immunoprecipitation, RNA interference, aconitase activity assay, IRP activity assay\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization with functional consequence, co-IP, multiple functional readouts; single lab\",\n      \"pmids\": [\"19454487\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Mammalian frataxin interacts with a preformed ISCU/NFS1/ISD11 core complex (not individual components) to form a stable quaternary complex of ~190 kDa; this interaction defines the essential function of frataxin in Fe-S cluster biosynthesis.\",\n      \"method\": \"Co-immunoprecipitation (in vivo and in vitro), heterologous expression system, size-exclusion chromatography\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — combined in vitro reconstitution and in vivo co-IP with complex isolation; single lab\",\n      \"pmids\": [\"21298097\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"A homozygous missense mutation R68L in human LYRM4/ISD11 causes combined OXPHOS deficiency (complexes I, II, III) and impairs Fe/S protein assembly; mutant ISD11 only partially complements yeast ISD11 deletion, and co-expression of mutant ISD11 with NFS1 yields nearly absent l-cysteine desulfurase activity in vitro.\",\n      \"method\": \"MitoExome sequencing, Sanger sequencing, yeast complementation assay, in vitro cysteine desulfurase activity assay with mutant protein\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro enzymatic assay with mutant protein, yeast complementation, patient biochemical data; multiple orthogonal methods\",\n      \"pmids\": [\"23814038\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Key ISD11 residues in helix 1 (Phe-40), helix 3 (Leu-63, Arg-68, Gln-69, Ile-72, Tyr-76), and C-terminal segment (Leu-81, Glu-84) are critical for interaction with NFS1; mutations at these sites reduce NFS1 stability, cause NFS1 aggregation, deplete ISCU levels, impair Fe/S cluster biosynthesis, reduce ETC complex activity, and diminish mitochondrial respiration. The disease mutation R68L/R68A reduces ISD11-NFS1 complex stability and causes mitochondrial iron accumulation and ROS elevation.\",\n      \"method\": \"Site-directed mutagenesis, co-immunoprecipitation, NFS1 aggregation assay, aconitase activity, ETC complex activity assays, mitochondrial respiration measurements, iron/ROS detection\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — systematic mutagenesis with multiple functional readouts (co-IP, aggregation, enzyme activity, respiration) in a single rigorous study\",\n      \"pmids\": [\"26342079\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal and EM structures of the human NFS1-ISD11-ACP (SDA) complex reveal that ISD11 subunits form the dimeric core of the complex (not NFS1 as in prokaryotes); the 4'-phosphopantetheine-conjugated acyl group of ACP occupies the hydrophobic core of ISD11, explaining ACP's role in stabilizing ISD11; the architecture creates an incompletely formed substrate channel and solvent-exposed PLP cofactor, explaining why FXN acts as an allosteric activator in eukaryotes.\",\n      \"method\": \"X-ray crystallography, cryo-EM, enzyme kinetic assays, cell-based complementation studies\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution crystal structure and cryo-EM validated by kinetics and cell-based assays; multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"28634302\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"When NFS1 and ISD11 are co-expressed in E. coli, the active preparation contains E. coli acyl carrier protein (ACP) in a stoichiometric [Acp]2:[ISD11]2:[NFS1]2 complex; E. coli ACP can substitute for human ACP in supporting Fe/S cluster assembly in vitro.\",\n      \"method\": \"Recombinant co-expression, mass spectrometry stoichiometry determination, in vitro Fe/S cluster assembly assay\",\n      \"journal\": \"ACS chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — reconstituted complex with defined stoichiometry and functional in vitro assay; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"28233492\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"The first 10 N-terminal amino acids of ISD11, including the conserved LYR motif, are indispensable for NFS1 activity and for forming a stable, active complex with NFS1; N-terminal truncations also disrupt mitochondrial targeting.\",\n      \"method\": \"In vitro purified protein interaction assays, NFS1 activity assays with N-terminal ISD11 mutants, cell-based subcellular localization studies\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — in vitro and in vivo studies with defined N-terminal mutants and functional readouts; single lab\",\n      \"pmids\": [\"28271877\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Isd11 has a profound effect on the oligomeric state of Nfs1: the presence of Isd11 alters the quaternary structure of the eukaryotic cysteine desulfurase complex.\",\n      \"method\": \"Biochemical characterization of oligomeric state (size-exclusion chromatography / biophysical analysis) with and without Isd11\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single biophysical method, single lab, limited mechanistic follow-up\",\n      \"pmids\": [\"24045011\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Human ISD11 alone exists in solution as an equilibrium of monomeric, dimeric, and tetrameric species; recombinant ISD11 expressed in E. coli co-purifies with bacterial IscS (the prokaryotic NFS1 ortholog) in a weak but specific interaction, indicating conservation of the desulfurase-binding surface.\",\n      \"method\": \"Analytical ultracentrifugation/gel filtration, co-purification from E. coli, binding specificity analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — co-purification and biophysical characterization; single lab, limited functional follow-up\",\n      \"pmids\": [\"27427956\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Human mitochondrial ACP and ISD11 form a soluble, structured, and stable complex when co-expressed in E. coli; ACP plays a key role in ISD11 folding and stability in vitro; the ACP-ISD11 complex binds NFS1 and modulates its cysteine desulfurase activity.\",\n      \"method\": \"Recombinant co-expression, co-purification, NFS1 activity assay, structural characterization\",\n      \"journal\": \"ACS chemical biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — reconstituted complex with functional enzyme activity assay; single lab\",\n      \"pmids\": [\"29737835\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Crystal structure of the human mitochondrial ACP-ISD11 heterodimer at 2.0 Å resolution reveals stabilization via ionic interactions, hydrogen bonds, and apolar contacts; the 4'-phosphopantetheine-acyl chain of ACP interacts with specific ISD11 residues, modulating ISD11 foldability; the ACP-ISD11 complex interacts with NFS1 yielding an active enzyme that is further activated by frataxin and ISCU.\",\n      \"method\": \"X-ray crystallography (2.0 Å), molecular dynamics simulations, NFS1 activity assay, protein-protein interaction assay\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — high-resolution crystal structure with functional enzyme assay and MD validation; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"31664822\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"In Trypanosoma brucei, Isd11 localizes to the mitochondrion and is required not only for Fe/S cluster assembly but also for both cytoplasmic and mitochondrial tRNA thiolation, placing Isd11 at the center of sulfur transfer pathways that connect Fe/S metabolism and tRNA modification.\",\n      \"method\": \"RNA interference (genetic depletion), subcellular fractionation/localization, biochemical tRNA thiolation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — genetic depletion with functional tRNA thiolation assay in a divergent eukaryote; single lab\",\n      \"pmids\": [\"20442400\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Elevated LYRM4 expression enhances the enzymatic activity of succinate dehydrogenase (SDH), promoting fumarate accumulation in hepatocellular carcinoma cells.\",\n      \"method\": \"Functional genomics (TUIFGA), SDH enzymatic activity assay, cellular metabolite measurement\",\n      \"journal\": \"Archives of biochemistry and biophysics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, limited mechanistic follow-up in abstract, no direct biochemical reconstitution described\",\n      \"pmids\": [\"40320061\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LYRM4/ISD11 is a small LYR-motif protein that forms the dimeric core of the eukaryote-specific NFS1-ISD11-ACP (SDA) cysteine desulfurase complex in mitochondria: ISD11 stabilizes NFS1 against aggregation and, together with acyl carrier protein (ACP) whose phosphopantetheine-acyl chain occupies the hydrophobic core of ISD11, establishes the quaternary architecture required for sulfur mobilization; the SDA complex then recruits ISCU2, frataxin (as an allosteric activator), and ferredoxin to assemble Fe/S clusters, with defined ISD11 residues (including the N-terminal LYR motif and helix-3 residue R68) being critical for NFS1 interaction, complex stability, and downstream Fe/S-dependent respiratory chain function.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LYRM4 (ISD11) is a small LYR-motif mitochondrial protein that functions as an essential eukaryotic component of the cysteine desulfurase machinery that initiates iron-sulfur (Fe/S) cluster biogenesis [#0, #1]. It forms a stable complex with the cysteine desulfurase NFS1 (Nfs1/ISCS), stabilizing the desulfurase against aggregation and altering its oligomeric state, such that loss of ISD11 abrogates Fe/S cluster loading onto the Isu/ISCU scaffold [#0, #1, #10]. In the assembled NFS1-ISD11-ACP (SDA) complex, ISD11 subunits form the dimeric core of the eukaryotic enzyme, and the 4'-phosphopantetheine-acyl chain of acyl carrier protein (ACP) occupies the hydrophobic core of ISD11, an interaction required for ISD11 folding and stability; this architecture leaves an incompletely formed substrate channel and solvent-exposed PLP cofactor, accounting for frataxin's role as an allosteric activator in eukaryotes [#7, #8, #13]. The SDA complex assembles with ISCU and frataxin into a stable quaternary complex, and ISD11 residues including the N-terminal LYR motif and helix-3 Arg-68 are critical for NFS1 interaction, complex stability, and downstream Fe/S-dependent respiratory chain function [#4, #6, #9]. Through its control of Fe/S cluster assembly, ISD11 governs the activity of aconitases and the electron transport chain and influences cellular iron homeostasis via IRP regulation [#2, #3]. A homozygous R68L missense mutation in human LYRM4 causes combined OXPHOS deficiency by destabilizing the ISD11-NFS1 complex and abolishing cysteine desulfurase activity [#5, #6].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Established that ISD11 is an indispensable, eukaryote-specific partner of the cysteine desulfurase NFS1/Nfs1 acting at the earliest step of Fe/S cluster biogenesis, answering whether a dedicated factor stabilizes the desulfurase.\",\n      \"evidence\": \"Genetic depletion in yeast with co-IP, enzymatic activity assays, iron incorporation, and Isu scaffold loading, replicated by two independent labs\",\n      \"pmids\": [\"16341090\", \"16341089\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the structural basis of NFS1 stabilization\", \"Stoichiometry and full complex composition not resolved\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Connected human ISD11 to frataxin and to disease, showing the desulfurase complex is a target of Friedreich's ataxia mutations and a regulator of cellular iron.\",\n      \"evidence\": \"Co-IP/mass spectrometry, siRNA knockdown, aconitase and iron content assays in mammalian cells\",\n      \"pmids\": [\"17331979\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether frataxin binds ISD11 directly or via the core complex unresolved here\", \"Single lab\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Demonstrated that human ISD11 controls both mitochondrial and cytosolic Fe/S-dependent enzymes and iron-regulatory protein activity, linking it to whole-cell iron homeostasis.\",\n      \"evidence\": \"Subcellular fractionation, co-IP with NFS1/ISCS, RNAi, aconitase and IRP activity assays\",\n      \"pmids\": [\"19454487\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reported nuclear localization not mechanistically explained\", \"Single lab\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Showed frataxin engages a preformed ISCU/NFS1/ISD11 core rather than individual components, defining the quaternary complex frataxin acts upon.\",\n      \"evidence\": \"In vivo and in vitro co-IP with size-exclusion chromatography of a ~190 kDa complex\",\n      \"pmids\": [\"21298097\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not resolve subunit arrangement or stoichiometry\", \"ACP not yet identified as a subunit\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identified a disease-causing LYRM4 mutation (R68L) and established ISD11's effect on the oligomeric state of the desulfurase, tying a specific residue to enzyme function and OXPHOS.\",\n      \"evidence\": \"MitoExome/Sanger sequencing, yeast complementation, in vitro cysteine desulfurase assay with mutant; separate biophysical oligomeric-state analysis\",\n      \"pmids\": [\"23814038\", \"24045011\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural mechanism by which R68L destabilizes the complex not defined at this stage\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Mapped the ISD11 surface required for NFS1 binding through systematic mutagenesis, defining residues whose loss causes NFS1 aggregation, ISCU depletion, and respiratory failure.\",\n      \"evidence\": \"Site-directed mutagenesis with co-IP, aggregation assays, ETC complex activity, respiration, and iron/ROS measurements\",\n      \"pmids\": [\"26342079\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Lacked atomic structure to interpret residue contributions\", \"ACP contribution not yet incorporated\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Solved the architecture of the SDA complex, revealing ISD11 dimers as the core, ACP's acyl chain buried in ISD11, and the structural basis for frataxin acting as an allosteric activator.\",\n      \"evidence\": \"X-ray crystallography and cryo-EM with enzyme kinetics and cell-based complementation; recombinant co-expression with defined [ACP]2:[ISD11]2:[NFS1]2 stoichiometry and in vitro Fe/S assays; N-terminal LYR-motif mutagenesis\",\n      \"pmids\": [\"28634302\", \"28233492\", \"28271877\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Dynamics of substrate channel formation during catalysis not captured\", \"How acyl-chain identity tunes activity not resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Established ACP as a folding chaperone for ISD11 and confirmed the ACP-ISD11 module binds and modulates NFS1 activity, clarifying why ACP is required for complex stability.\",\n      \"evidence\": \"Recombinant co-expression, co-purification, structural characterization, and NFS1 activity assays\",\n      \"pmids\": [\"29737835\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Physiological acyl-chain occupancy in vivo not quantified\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Provided a high-resolution ACP-ISD11 heterodimer structure detailing the interface and acyl-chain contacts that modulate ISD11 foldability and enable NFS1 activation by frataxin and ISCU.\",\n      \"evidence\": \"2.0 Å X-ray crystallography, molecular dynamics, NFS1 activity and interaction assays\",\n      \"pmids\": [\"31664822\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Conformational changes upon frataxin/ISCU binding not captured in this structure\", \"Single lab\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Extended ISD11 function beyond Fe/S clusters by showing it is required for cytoplasmic and mitochondrial tRNA thiolation in Trypanosoma brucei, placing it at a sulfur-transfer hub.\",\n      \"evidence\": \"RNAi depletion, subcellular localization, and tRNA thiolation assays in a divergent eukaryote\",\n      \"pmids\": [\"20442400\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct role in human tRNA thiolation not demonstrated\", \"Single lab, divergent organism\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Linked elevated LYRM4 to altered metabolism in hepatocellular carcinoma via enhanced SDH activity and fumarate accumulation.\",\n      \"evidence\": \"Functional genomics, SDH activity assay, and metabolite measurement in HCC cells\",\n      \"pmids\": [\"40320061\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct biochemical reconstitution described\", \"Mechanism connecting LYRM4 to SDH activity not established\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the SDA complex dynamically coordinates frataxin and ISCU recruitment, ferredoxin electron delivery, and sulfur channeling during catalytic Fe/S cluster turnover, and whether human ISD11 directly supports tRNA thiolation, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No catalytic-cycle structure of the full assembly\", \"Human tRNA thiolation role untested\", \"Regulation of LYRM4 expression in disease contexts unclear\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 5, 6, 13]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 7, 12, 13]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [3, 9, 14]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\"NFS1-ISD11-ACP (SDA) cysteine desulfurase complex\", \"ISCU/NFS1/ISD11 core complex\"],\n    \"partners\": [\"NFS1\", \"NDUFAB1\", \"ISCU\", \"FXN\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}