Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0016226 iron-sulfur cluster assembly	IBA GO_REF:0000033	ACCEPT	Summary: Iron-sulfur cluster assembly is the core biological process for FXN. FXN functions within the mitochondrial ISC assembly complex to promote de novo [2Fe-2S] cluster synthesis. This annotation is well-supported by phylogenetic inference and extensive experimental evidence. Reason: FXN is a key component of the mitochondrial iron-sulfur cluster assembly machinery. Multiple studies demonstrate its role in accelerating persulfide transfer from NFS1 to ISCU during [2Fe-2S] cluster assembly (PMID:12785837, PMID:24971490, PMID:29576242). The IBA annotation correctly reflects the conserved function across eukaryotes. Supporting Evidence: PMID:12785837 Provision of holo frataxin and inorganic sulfide is sufficient for cluster assembly in up to 70% yield. PMID:24971490 FXN accelerates the accumulation of sulfur on ISCU2 and that the resulting persulfide species is viable in the subsequent synthesis of Fe-S clusters. file:human/FXN/FXN-deep-research-falcon.md model: Edison Scientific Literature
GO:0008198 ferrous iron binding	IBA GO_REF:0000033	ACCEPT	Summary: Ferrous iron binding is a well-established molecular function of frataxin. FXN tightly binds a single Fe2+ ion but not Fe3+, and this iron is released during Fe-S cluster assembly. Reason: FXN binds Fe2+ with high affinity. NMR and ITC studies demonstrate specific binding of Fe2+ (K_D approximately 55 microM) but not Fe3+ (PMID:12785837, PMID:29576242). The iron-binding site is located on the alpha1-beta1 face of the protein. Supporting Evidence: PMID:29576242 FXN tightly binds a single Fe2+ but not Fe3+. PMID:12785837 Iron binding to frataxin has been quantitated by iron-dependent fluorescence measurements [K(D)(Fe(3+)) approximately 11.7 microM; (K(D)(Fe(2+)) approximately 55.0 microM] and isothermal titration calorimetry (ITC) [K(D)(Fe(3+)) approximately 10.2 microM]
GO:0005739 mitochondrion	IBA GO_REF:0000033	ACCEPT	Summary: Mitochondrial localization is strongly supported. FXN is synthesized as a precursor with an N-terminal targeting sequence and processed to the mature form in mitochondria. Reason: Multiple experimental studies confirm mitochondrial localization (PMID:9302253, PMID:9241270, PMID:21298097). The protein is processed by mitochondrial processing peptidase in two steps to yield the mature mitochondrial form. Supporting Evidence: PMID:21298097 The main interactors from mitochondrial HeLa cell extract of a C-terminal or N-terminal tagged human mature frataxin (hFXN81-210) are the core components of the de novo Fe-S cluster biosynthesis, ISCU, NFS1 and ISD11.
GO:0008199 ferric iron binding	IBA GO_REF:0000033	MARK AS OVER ANNOTATED	Summary: Ferric iron binding by FXN is controversial. Recent NMR studies show FXN binds Fe2+ but not Fe3+, though earlier studies reported Fe3+ binding. Reason: While earlier studies suggested FXN binds both Fe2+ and Fe3+ (PMID:12785837), more recent NMR studies (PMID:29576242) demonstrate that FXN binds Fe2+ but not Fe3+. When Fe2+ is oxidized to Fe3+, it dissociates from FXN. The physiologically relevant form appears to be Fe2+-bound FXN. Supporting Evidence: PMID:29576242 FXN tightly binds a single Fe2+ but not Fe3+... the addition of a 5-fold excess of FeCl3 did not lead to significant chemical shift perturbations... oxidized Fe2+ lost affinity to FXN.
GO:0034986 iron chaperone activity	IBA GO_REF:0000033	ACCEPT	Summary: Iron chaperone activity is a core molecular function of FXN. The protein delivers iron to multiple targets including ISCU for Fe-S cluster assembly and ferrochelatase for heme biosynthesis. Reason: FXN functions as an iron chaperone, delivering Fe2+ to the ISC assembly complex and to ferrochelatase for heme biosynthesis (PMID:15123683, PMID:12785837). Iron is released from FXN only when cysteine desulfurase is activated by both L-cysteine and reductant. Supporting Evidence: PMID:15123683 Herein we demonstrate Hs holofrataxin to be a high affinity iron binding partner for Hs ferrochelatase that is capable of both delivering iron to ferrochelatase and mediating the terminal step in mitochondrial heme biosynthesis PMID:29576242 Although the present results do not prove that the released iron is picked up by ISCU and used for Fe-S cluster formation, we have shown that Fe2+-FXN can serve as the sole iron donor for this process in vitro
GO:0051537 2 iron, 2 sulfur cluster binding	IBA GO_REF:0000033	UNDECIDED	Summary: Evidence for [2Fe-2S] cluster binding by FXN is limited. FXN is involved in [2Fe-2S] cluster assembly on ISCU but whether it binds the cluster itself is uncertain. Reason: While PMID:12785837 reported some evidence for [2Fe-2S] binding, the primary function of FXN is to deliver iron and activate sulfur transfer for cluster assembly on ISCU, not to bind the assembled cluster. More evidence would be needed to confirm this annotation.
GO:0004322 ferroxidase activity	IEA GO_REF:0000120	ACCEPT	Summary: Ferroxidase activity has been demonstrated for the oligomeric form of FXN in vitro. The monomeric form does not have this activity. Reason: The oligomeric form of human FXN has ferroxidase activity (EC 1.16.3.1) that catalyzes oxidation of Fe2+ to Fe3+, which may help detoxify redox-active iron (PMID:15641778). However, the physiological relevance is uncertain as the monomer is likely the predominant form. Supporting Evidence: PMID:15641778 The assembled protein has ferroxidase activity and detoxifies redox-active iron by sequestering it in a protein-protected compartment.
GO:0005739 mitochondrion	IEA GO_REF:0000120	ACCEPT	Summary: Redundant with IBA annotation for mitochondrion. Reason: Correct localization, supported by multiple experimental studies.
GO:0005829 cytosol	IEA GO_REF:0000044	ACCEPT	Summary: An extramitochondrial form of frataxin exists in the cytosol. This form modulates the RNA-binding activity of cytosolic aconitase (ACO1/IRP1). Reason: Extramitochondrial frataxin has been detected and characterized (PMID:20053667, PMID:16608849). It may contribute to oxidative stress resistance and regulate the cytosolic aconitase/IRP1 switch. Supporting Evidence: PMID:20053667 Molecular control of the cytosolic aconitase/IRP1 switch by extramitochondrial frataxin.
GO:0006783 heme biosynthetic process	IEA GO_REF:0000043	KEEP AS NON CORE	Summary: FXN delivers iron to ferrochelatase for the terminal step of heme biosynthesis. This is a secondary function to its primary role in Fe-S cluster assembly. Reason: FXN functions as an iron donor for ferrochelatase in the final step of heme biosynthesis (PMID:15123683). However, this appears to be a secondary function; the primary role is in Fe-S cluster assembly. Supporting Evidence: PMID:15123683 A general regulatory mechanism for mitochondrial iron metabolism is described that defines frataxin involvement in both heme and iron-sulfur cluster biosyntheses.
GO:0006811 monoatomic ion transport	IEA GO_REF:0000043	MARK AS OVER ANNOTATED	Summary: This is a very general term. FXN does not function as a transporter but as an iron chaperone that delivers iron within the mitochondrial matrix. Reason: FXN functions as an iron chaperone, not an ion transporter. The term monoatomic ion transport is too general and misleading for FXN's actual function.
GO:0006826 iron ion transport	IEA GO_REF:0000043	MODIFY	Summary: FXN is an iron chaperone rather than a transporter. It delivers iron within the mitochondrial matrix to target proteins. Reason: FXN delivers iron to ISCU and ferrochelatase but does not transport iron across membranes. A more appropriate term would be iron chaperone activity (GO:0034986), which is already annotated. Proposed replacements: iron chaperone activity
GO:0006879 intracellular iron ion homeostasis	IEA GO_REF:0000002	KEEP AS NON CORE	Summary: FXN deficiency leads to mitochondrial iron accumulation and dysregulation of iron homeostasis. However, this is a downstream consequence rather than a direct function. Reason: FXN loss leads to disrupted iron homeostasis and mitochondrial iron accumulation (PMID:18160053). However, iron homeostasis regulation is an indirect consequence of FXN's role in Fe-S cluster assembly rather than a direct molecular function. Supporting Evidence: PMID:18160053 The effects of frataxin silencing in HeLa cells are rescued by the expression of human mitochondrial ferritin.
GO:0007005 mitochondrion organization	IEA GO_REF:0000117	MARK AS OVER ANNOTATED	Summary: Mitochondrial organization is affected by FXN deficiency, but this is a downstream consequence of impaired Fe-S cluster biogenesis. Reason: While FXN deficiency affects mitochondrial structure, this is a secondary consequence of impaired Fe-S cluster assembly affecting respiratory chain complexes rather than a direct function of FXN in mitochondrial organization.
GO:0008199 ferric iron binding	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: Duplicate of IBA annotation. Evidence for Fe3+ binding is weak. Reason: Recent NMR evidence shows FXN binds Fe2+ but not Fe3+ (PMID:29576242). Earlier reports of Fe3+ binding may reflect oxidation of bound Fe2+.
GO:0016226 iron-sulfur cluster assembly	IEA GO_REF:0000002	ACCEPT	Summary: Duplicate of IBA annotation. Core function well supported. Reason: Core biological process for FXN, well supported by multiple studies.
GO:0016491 oxidoreductase activity	IEA GO_REF:0000043	ACCEPT	Summary: FXN has ferroxidase activity (EC 1.16.3.1) in its oligomeric form, which is a type of oxidoreductase activity. Reason: The oligomeric form of FXN has ferroxidase activity (PMID:15641778), which catalyzes the oxidation of Fe2+ to Fe3+. This is an oxidoreductase activity.
GO:0030003 intracellular monoatomic cation homeostasis	IEA GO_REF:0000117	MARK AS OVER ANNOTATED	Summary: This is a general term. FXN's effect on iron homeostasis is indirect through its role in Fe-S cluster assembly. Reason: Very general term; effect on homeostasis is indirect.
GO:0046872 metal ion binding	IEA GO_REF:0000043	ACCEPT	Summary: Correct but overly general. FXN specifically binds ferrous iron. More specific terms (ferrous iron binding) are already annotated. Reason: Correct that FXN binds metal ions (specifically Fe2+), but the more specific term ferrous iron binding (GO:0008198) is preferable.
GO:0098771 inorganic ion homeostasis	IEA GO_REF:0000117	MARK AS OVER ANNOTATED	Summary: Very general term, indirect effect. Reason: Very general term; FXN's effect on ion homeostasis is indirect through Fe-S cluster assembly.
GO:0005515 protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	MARK AS OVER ANNOTATED	Summary: Generic protein binding term from high-throughput interactome study. FXN binds specific partners including NFS1, ISCU, ISD11, and ferrochelatase. Reason: Protein binding is too generic. FXN has specific, functionally relevant interactions with the ISC assembly complex components (NFS1, ISD11, ISCU) and ferrochelatase. Supporting Evidence: PMID:32296183 Apr 8. A reference map of the human binary protein interactome.
GO:0005515 protein binding	IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ...	MARK AS OVER ANNOTATED	Summary: Generic protein binding from interactome study. Reason: Protein binding is too generic and uninformative for FXN. Supporting Evidence: PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
GO:0044572 [4Fe-4S] cluster assembly	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: FXN is directly involved in [2Fe-2S] cluster assembly on ISCU. The [4Fe-4S] clusters are formed downstream by combination of [2Fe-2S] clusters. Reason: FXN's direct role is in [2Fe-2S] cluster assembly. [4Fe-4S] cluster formation occurs downstream and depends on prior [2Fe-2S] cluster synthesis, so FXN acts upstream of this process. Supporting Evidence: PMID:29576242 Our current model of the mechanism of mitochondrial Fe-S cluster assembly consists of the following steps
GO:0099128 mitochondrial [2Fe-2S] assembly complex	IEA GO_REF:0000107	ACCEPT	Summary: FXN is a component of the mitochondrial [2Fe-2S] assembly complex. Multiple cryo-EM and biochemical studies confirm this. Reason: FXN is a confirmed component of the SDUF complex (NFS1-ISD11-ACP-ISCU-FXN) that assembles [2Fe-2S] clusters (PMID:31101807, PMID:21298097). Supporting Evidence: PMID:31101807 Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism. PMID:21298097 the essential function of mammalian frataxin consists in interacting with the preformed ISCU/NFS1/ISD11 complex
GO:0005739 mitochondrion	IDA GO_REF:0000052	ACCEPT	Summary: Mitochondrial localization confirmed by immunofluorescence. Reason: Well-established mitochondrial localization.
GO:0005829 cytosol	IDA GO_REF:0000052	ACCEPT	Summary: Cytosolic localization of extramitochondrial frataxin confirmed. Reason: An extramitochondrial form of frataxin exists in the cytosol (PMID:20053667, PMID:16608849).
GO:0016226 iron-sulfur cluster assembly	TAS Reactome:R-HSA-1362409	ACCEPT	Summary: Reactome annotation for mitochondrial iron-sulfur cluster biogenesis. Reason: Core function well supported by Reactome pathway curation.
GO:0034551 mitochondrial respiratory chain complex III assembly	TAS Reactome:R-HSA-9865881	KEEP AS NON CORE	Summary: FXN contributes to Complex III assembly by providing Fe-S clusters. This is a downstream effect of its Fe-S cluster assembly function. Reason: FXN contributes to Complex III assembly indirectly through its role in Fe-S cluster biosynthesis. The Rieske protein (UQCRFS1) requires a [2Fe-2S] cluster.
GO:0005739 mitochondrion	NAS PMID:27519411 Architecture of the Human Mitochondrial Iron-Sulfur Cluster ...	ACCEPT	Summary: Mitochondrial localization from structural study of ISC complex. Reason: Well-established mitochondrial localization. Supporting Evidence: PMID:27519411 Epub 2016 Aug 12. Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery.
GO:0016226 iron-sulfur cluster assembly	NAS PMID:29097656 Structure and functional dynamics of the mitochondrial Fe/S ...	ACCEPT	Summary: Fe-S cluster assembly role from structural study. Reason: Core function confirmed by structural studies. Supporting Evidence: PMID:29097656 Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex.
GO:0008198 ferrous iron binding	TAS Reactome:R-HSA-1362416	ACCEPT	Summary: Reactome annotation for frataxin binding iron. Reason: Core molecular function well supported.
GO:0016226 iron-sulfur cluster assembly	IDA PMID:12785837 Iron-sulfur cluster biosynthesis. Characterization of fratax...	ACCEPT	Summary: Direct experimental evidence from Yoon and Cowan demonstrating FXN as iron donor for [2Fe-2S] cluster assembly on ISU-type proteins. Reason: Key primary study demonstrating FXN's role in Fe-S cluster assembly with direct biochemical assays. Supporting Evidence: PMID:12785837 Holo frataxin is also shown to mediate the transfer of iron from holo frataxin to nucleation sites for [2Fe-2S] cluster formation on ISU.
GO:0006783 heme biosynthetic process	IDA PMID:15123683 Frataxin-mediated iron delivery to ferrochelatase in the fin...	KEEP AS NON CORE	Summary: Direct evidence that FXN delivers iron to ferrochelatase for heme biosynthesis. Reason: FXN serves as iron donor for ferrochelatase, but this is secondary to its primary role in Fe-S cluster assembly. Supporting Evidence: PMID:15123683 Herein we demonstrate Hs holofrataxin to be a high affinity iron binding partner for Hs ferrochelatase that is capable of both delivering iron to ferrochelatase and mediating the terminal step in mitochondrial heme biosynthesis
GO:0008047 enzyme activator activity	IDA PMID:15123683 Frataxin-mediated iron delivery to ferrochelatase in the fin...	ACCEPT	Summary: FXN activates ferrochelatase by delivering iron. It also activates the cysteine desulfurase NFS1 in the ISC complex. Reason: FXN activates both ferrochelatase (PMID:15123683) and the cysteine desulfurase NFS1 (PMID:24971490, PMID:28634302). This allosteric activation is a core function. Supporting Evidence: PMID:24971490 Previous in vitro results revealed a role for human FXN in activating the cysteine desulfurase and Fe-S cluster biosynthesis activities of the Fe-S assembly complex. PMID:15123683 2004 Apr 27. Frataxin-mediated iron delivery to ferrochelatase in the final step of heme biosynthesis.
GO:0051604 protein maturation	IMP PMID:15509595 Iron-sulfur protein maturation in human cells - evidence for...	KEEP AS NON CORE	Summary: FXN is required for maturation of Fe-S proteins. This reflects its role in Fe-S cluster assembly and transfer. Reason: FXN contributes to Fe-S protein maturation through its role in cluster assembly, but protein maturation is not its direct molecular function. Supporting Evidence: PMID:15509595 Oct 27. Iron-sulfur protein maturation in human cells: evidence for a function of frataxin.
GO:0008047 enzyme activator activity	IDA PMID:28634302 Structure of human Fe-S assembly subcomplex reveals unexpect...	ACCEPT	Summary: Structural evidence for FXN activating cysteine desulfurase. Reason: FXN functions as an allosteric activator of the cysteine desulfurase complex, accelerating sulfur transfer from NFS1 to ISCU. Supporting Evidence: PMID:28634302 Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions.
GO:0008047 enzyme activator activity	IDA PMID:38627381 Mechanism and structural dynamics of sulfur transfer during ...	ACCEPT	Summary: Recent structural study showing FXN's activating role in sulfur transfer. Reason: Recent cryo-EM study demonstrates FXN optimally positions residues for rapid persulfide transfer from NFS1 to ISCU. Supporting Evidence: PMID:38627381 Mechanism and structural dynamics of sulfur transfer during de novo [2Fe-2S] cluster assembly on ISCU2.
GO:0044571 [2Fe-2S] cluster assembly	IDA PMID:29491838 Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Dro...	ACCEPT	Summary: This annotation is from FlyBase citing PMID:29491838, which is about Drosophila Fe-S cluster metabolism. The annotation to human FXN may be an inference from fly data. Reason: While the reference is about Drosophila, the annotation of human FXN's role in [2Fe-2S] cluster assembly is well-supported by other studies (PMID:24971490, PMID:29576242). FXN is a core component of the ISC complex required for [2Fe-2S] cluster synthesis. Supporting Evidence: PMID:24971490 FXN accelerates the accumulation of sulfur on ISCU2 and that the resulting persulfide species is viable in the subsequent synthesis of Fe-S clusters. PMID:29491838 Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life Cycle by Controlling Cell Metabolism.
GO:0044571 [2Fe-2S] cluster assembly	IDA PMID:38627381 Mechanism and structural dynamics of sulfur transfer during ...	ACCEPT	Summary: Recent structural study of [2Fe-2S] cluster assembly mechanism. Reason: Core function demonstrated by recent high-resolution structural studies. Supporting Evidence: PMID:38627381 Mechanism and structural dynamics of sulfur transfer during de novo [2Fe-2S] cluster assembly on ISCU2.
GO:0005739 mitochondrion	HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an...	ACCEPT	Summary: High-throughput proteomics confirming mitochondrial localization. Reason: Well-established mitochondrial localization. Supporting Evidence: PMID:34800366 Epub 2021 Nov 19. Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.
GO:0005759 mitochondrial matrix	IC PMID:29491838 Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Dro...	ACCEPT	Summary: FXN functions in the mitochondrial matrix as part of the ISC assembly complex. Reason: The ISC assembly complex operates in the mitochondrial matrix, and FXN is a component of this complex. Supporting Evidence: PMID:29491838 Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life Cycle by Controlling Cell Metabolism.
GO:0005515 protein binding	IPI PMID:31101807 Structure of the human frataxin-bound iron-sulfur cluster as...	ACCEPT	Summary: Interaction with ISCU and NFS1 demonstrated in structural study. This represents functionally relevant binding. Reason: This annotation reflects the specific, functionally important interactions of FXN with ISCU (Q9H1K1) and NFS1 (Q9Y697) demonstrated by cryo-EM. Supporting Evidence: PMID:31101807 Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism.
GO:0099128 mitochondrial [2Fe-2S] assembly complex	IDA PMID:29491838 Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Dro...	ACCEPT	Summary: FXN is a component of the mitochondrial [2Fe-2S] assembly complex. Reason: Core cellular component for FXN, well established by multiple studies. Supporting Evidence: PMID:29491838 Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life Cycle by Controlling Cell Metabolism.
GO:0034986 iron chaperone activity	TAS Reactome:R-HSA-9866272	ACCEPT	Summary: Reactome annotation for iron chaperone function in cluster assembly. Reason: Core molecular function well supported.
GO:0099128 mitochondrial [2Fe-2S] assembly complex	IDA PMID:31101807 Structure of the human frataxin-bound iron-sulfur cluster as...	ACCEPT	Summary: Cryo-EM structure confirms FXN as component of ISC complex. Reason: High-resolution cryo-EM structure demonstrates FXN binding to the ISC complex. Supporting Evidence: PMID:31101807 Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism.
GO:0044571 [2Fe-2S] cluster assembly	IDA PMID:24971490 Human frataxin activates Fe-S cluster biosynthesis by facili...	ACCEPT	Summary: Direct biochemical evidence that FXN accelerates [2Fe-2S] cluster assembly by facilitating sulfur transfer. Reason: Key study demonstrating FXN's allosteric activation of sulfur transfer from NFS1 to ISCU for [2Fe-2S] cluster assembly. Supporting Evidence: PMID:24971490 FXN accelerates the accumulation of sulfur on ISCU2 and that the resulting persulfide species is viable in the subsequent synthesis of Fe-S clusters.
GO:0008198 ferrous iron binding	IDA PMID:29576242 Interactions of iron-bound frataxin with ISCU and ferredoxin...	ACCEPT	Summary: NMR evidence for specific Fe2+ binding. Reason: Detailed NMR study demonstrating specific binding of Fe2+ (but not Fe3+) to FXN. Supporting Evidence: PMID:29576242 FXN tightly binds a single Fe2+ but not Fe3+.
GO:0044571 [2Fe-2S] cluster assembly	IDA PMID:29576242 Interactions of iron-bound frataxin with ISCU and ferredoxin...	ACCEPT	Summary: NMR study demonstrating FXN's role in [2Fe-2S] cluster assembly. Reason: Core biological process well supported. Supporting Evidence: PMID:29576242 Epub 2018 Mar 15. Interactions of iron-bound frataxin with ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster assembly.
GO:0044572 [4Fe-4S] cluster assembly	IDA PMID:29576242 Interactions of iron-bound frataxin with ISCU and ferredoxin...	KEEP AS NON CORE	Summary: FXN contributes to [4Fe-4S] cluster assembly indirectly through [2Fe-2S] cluster synthesis. Reason: FXN's direct role is in [2Fe-2S] cluster assembly. [4Fe-4S] clusters form downstream by combination of [2Fe-2S] clusters. Supporting Evidence: PMID:29576242 Epub 2018 Mar 15. Interactions of iron-bound frataxin with ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster assembly.
GO:0044572 [4Fe-4S] cluster assembly	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: Inferred from mouse ortholog. Reason: Indirect contribution through [2Fe-2S] cluster synthesis.
GO:0005739 mitochondrion	IDA PMID:21298097 Mammalian frataxin - an essential function for cellular viab...	ACCEPT	Summary: Experimental evidence for mitochondrial localization. Reason: Well-established mitochondrial localization. Supporting Evidence: PMID:21298097 Mammalian frataxin: an essential function for cellular viability through an interaction with a preformed ISCU/NFS1/ISD11 iron-sulfur assembly complex.
GO:0099128 mitochondrial [2Fe-2S] assembly complex	IDA PMID:21298097 Mammalian frataxin - an essential function for cellular viab...	ACCEPT	Summary: Key study demonstrating FXN interacts with preformed ISCU/NFS1/ISD11 complex. Reason: Comprehensive study showing FXN is a component of the ISC assembly complex. Supporting Evidence: PMID:21298097 Our results demonstrate that frataxin interacts with a preformed ISCU/NFS1/ISD11 complex rather than with the individual components to form a stable quaternary complex.
GO:0005515 protein binding	IPI PMID:26702583 Mitochondrial Hspa9/Mortalin regulates erythroid differentia...	ACCEPT	Summary: Interaction with HSPA9/mortalin demonstrated. Reason: HSPA9 is a mitochondrial chaperone involved in Fe-S cluster transfer. The interaction with FXN is functionally relevant. Supporting Evidence: PMID:26702583 Dec 17. Mitochondrial Hspa9/Mortalin regulates erythroid differentiation via iron-sulfur cluster assembly.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-1362408	ACCEPT	Summary: Reactome annotation for mitochondrial matrix localization. Reason: The ISC complex operates in the mitochondrial matrix.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-1362416	ACCEPT	Summary: Duplicate Reactome annotation. Reason: Correct localization.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9854405	ACCEPT	Summary: Reactome annotation for frataxin transferring Fe2+ to ACO2. Reason: Correct localization.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9854984	ACCEPT	Summary: Reactome annotation for Fe-S cluster transfer to SDHB. Reason: Correct localization.
GO:0005759 mitochondrial matrix	TAS Reactome:R-HSA-9866272	ACCEPT	Summary: Reactome annotation for [2Fe-2S] insertion in UQCRFS1. Reason: Correct localization.
GO:0004322 ferroxidase activity	IDA PMID:15641778 Assembly of human frataxin is a mechanism for detoxifying re...	ACCEPT	Summary: Direct demonstration of ferroxidase activity for oligomeric FXN. Reason: The oligomeric form of FXN has ferroxidase activity that may help detoxify redox-active iron, though the monomer is likely the predominant functional form. Supporting Evidence: PMID:15641778 The assembled protein has ferroxidase activity and detoxifies redox-active iron by sequestering it in a protein-protected compartment.
GO:0051349 positive regulation of lyase activity	IDA PMID:20053667 Molecular control of the cytosolic aconitase/IRP1 switch by ...	KEEP AS NON CORE	Summary: Extramitochondrial frataxin modulates cytosolic aconitase (ACO1) activity. Reason: This activity of extramitochondrial frataxin is a secondary function. The primary role is in mitochondrial Fe-S cluster assembly. Supporting Evidence: PMID:20053667 Molecular control of the cytosolic aconitase/IRP1 switch by extramitochondrial frataxin.
GO:0070301 cellular response to hydrogen peroxide	IDA PMID:15641778 Assembly of human frataxin is a mechanism for detoxifying re...	KEEP AS NON CORE	Summary: Oligomeric FXN can detoxify redox-active iron and protect against oxidative stress. Reason: Protection against oxidative stress is a secondary consequence of FXN's iron sequestration activity. Supporting Evidence: PMID:15641778 However, the monomer is unable to prevent iron-catalyzed radical reactions and the formation of insoluble ferric iron oxides
GO:0043066 negative regulation of apoptotic process	IMP PMID:16608849 A pool of extramitochondrial frataxin that promotes cell sur...	KEEP AS NON CORE	Summary: Extramitochondrial frataxin contributes to cell survival and inhibits apoptosis. Reason: Anti-apoptotic function is associated with extramitochondrial frataxin and represents a secondary function. Supporting Evidence: PMID:16608849 2006 Apr 11. A pool of extramitochondrial frataxin that promotes cell survival.
GO:0090201 negative regulation of release of cytochrome c from mitochondria	IMP PMID:16608849 A pool of extramitochondrial frataxin that promotes cell sur...	KEEP AS NON CORE	Summary: FXN prevents cytochrome c release from mitochondria. Reason: This anti-apoptotic effect is a secondary consequence of FXN function. Supporting Evidence: PMID:16608849 2006 Apr 11. A pool of extramitochondrial frataxin that promotes cell survival.
GO:0034986 iron chaperone activity	IDA PMID:15123683 Frataxin-mediated iron delivery to ferrochelatase in the fin...	ACCEPT	Summary: Direct demonstration of iron chaperone activity - FXN delivers iron to ferrochelatase. Reason: Iron chaperone activity is a core molecular function of FXN, delivering iron to both ferrochelatase and the ISC assembly complex. Supporting Evidence: PMID:15123683 Herein we demonstrate Hs holofrataxin to be a high affinity iron binding partner for Hs ferrochelatase that is capable of both delivering iron to ferrochelatase and mediating the terminal step in mitochondrial heme biosynthesis
GO:0005759 mitochondrial matrix	ISS GO_REF:0000024	ACCEPT	Summary: Inferred from yeast ortholog. Reason: Correct localization based on conserved function.
GO:0005759 mitochondrial matrix	NAS PMID:17285345 N-terminal iron-mediated self-cleavage of human frataxin - r...	ACCEPT	Summary: Mitochondrial matrix localization from iron-binding study. Reason: Correct localization. Supporting Evidence: PMID:17285345 2007 Feb 7. N-terminal iron-mediated self-cleavage of human frataxin: regulation of iron binding and complex formation with target proteins.
GO:0008198 ferrous iron binding	IDA PMID:12785837 Iron-sulfur cluster biosynthesis. Characterization of fratax...	ACCEPT	Summary: Initial characterization of iron binding to frataxin. Reason: Core molecular function well demonstrated. Supporting Evidence: PMID:12785837 In this paper we demonstrate human frataxin to bind from six to seven iron ions.
GO:0008198 ferrous iron binding	IDA PMID:17285345 N-terminal iron-mediated self-cleavage of human frataxin - r...	ACCEPT	Summary: Iron binding study with N-terminal self-cleavage characterization. Reason: Core molecular function. Supporting Evidence: PMID:17285345 2007 Feb 7. N-terminal iron-mediated self-cleavage of human frataxin: regulation of iron binding and complex formation with target proteins.
GO:0008199 ferric iron binding	IDA PMID:12785837 Iron-sulfur cluster biosynthesis. Characterization of fratax...	MARK AS OVER ANNOTATED	Summary: Early study reporting ferric iron binding. Later NMR studies (PMID:29576242) show FXN preferentially binds Fe2+ not Fe3+. Reason: More recent NMR evidence demonstrates FXN binds Fe2+ but not Fe3+ (PMID:29576242). The earlier reports of Fe3+ binding may reflect oxidation of bound Fe2+. Supporting Evidence: PMID:12785837 Iron-sulfur cluster biosynthesis.
GO:0016540 protein autoprocessing	IDA PMID:12785837 Iron-sulfur cluster biosynthesis. Characterization of fratax...	REMOVE	Summary: FXN precursor undergoes two-step proteolytic processing by MPP to yield mature form. This is not autoprocessing but processing by mitochondrial processing peptidase. Reason: FXN is processed by mitochondrial processing peptidase (MPP), not by autoprocessing. The term is incorrect for FXN maturation. Supporting Evidence: PMID:12785837 Iron-sulfur cluster biosynthesis.
GO:0051537 2 iron, 2 sulfur cluster binding	IDA PMID:12785837 Iron-sulfur cluster biosynthesis. Characterization of fratax...	UNDECIDED	Summary: Some evidence for [2Fe-2S] binding was reported, but FXN's primary role is to facilitate cluster assembly on ISCU rather than to bind clusters itself. Reason: The evidence for [2Fe-2S] cluster binding by FXN is limited. More recent studies emphasize FXN's role in delivering iron and activating sulfur transfer rather than binding assembled clusters. Supporting Evidence: PMID:12785837 Iron-sulfur cluster biosynthesis.
GO:0005515 protein binding	IPI PMID:15123683 Frataxin-mediated iron delivery to ferrochelatase in the fin...	ACCEPT	Summary: Interaction with ferrochelatase (FECH/P22830) demonstrated. Reason: Functionally relevant interaction with ferrochelatase for iron delivery in heme biosynthesis. Supporting Evidence: PMID:15123683 Herein we demonstrate Hs holofrataxin to be a high affinity iron binding partner for Hs ferrochelatase that is capable of both delivering iron to ferrochelatase and mediating the terminal step in mitochondrial heme biosynthesis
GO:0005739 mitochondrion	IDA PMID:17468497 In vivo maturation of human frataxin.	ACCEPT	Summary: Experimental evidence for mitochondrial localization in vivo. Reason: Well-established mitochondrial localization. Supporting Evidence: PMID:17468497 Apr 27. In vivo maturation of human frataxin.
GO:0005829 cytosol	IDA PMID:17468497 In vivo maturation of human frataxin.	ACCEPT	Summary: Evidence for cytosolic localization of some FXN forms. Reason: Extramitochondrial frataxin exists in the cytosol. Supporting Evidence: PMID:17468497 Apr 27. In vivo maturation of human frataxin.
GO:0006879 intracellular iron ion homeostasis	IMP PMID:18160053 The effects of frataxin silencing in HeLa cells are rescued ...	KEEP AS NON CORE	Summary: FXN silencing disrupts iron homeostasis, rescued by mitochondrial ferritin expression. Reason: Effect on iron homeostasis is indirect through disrupted Fe-S cluster assembly. Supporting Evidence: PMID:18160053 The effects of frataxin silencing in HeLa cells are rescued by the expression of human mitochondrial ferritin.
GO:0008198 ferrous iron binding	IDA PMID:15123683 Frataxin-mediated iron delivery to ferrochelatase in the fin...	ACCEPT	Summary: Fe2+ binding demonstrated in context of ferrochelatase delivery. Reason: Core molecular function. Supporting Evidence: PMID:15123683 2004 Apr 27. Frataxin-mediated iron delivery to ferrochelatase in the final step of heme biosynthesis.
GO:0008199 ferric iron binding	IDA PMID:18537827 Dynamics, stability and iron-binding activity of frataxin cl...	MARK AS OVER ANNOTATED	Summary: Study of FRDA clinical mutants and iron binding. Reason: More recent NMR evidence (PMID:29576242) shows FXN binds Fe2+ but not Fe3+. Supporting Evidence: PMID:18537827 Dynamics, stability and iron-binding activity of frataxin clinical mutants.
GO:0010039 response to iron ion	IMP PMID:18424449 Iron-dependent regulation of frataxin expression - implicati...	KEEP AS NON CORE	Summary: FXN expression is regulated by iron levels. Reason: FXN is regulated by iron, but this describes regulation of FXN rather than its function. Supporting Evidence: PMID:18424449 Apr 17. Iron-dependent regulation of frataxin expression: implications for treatment of Friedreich ataxia.
GO:0005515 protein binding	IPI PMID:15961414 Frataxin interacts functionally with mitochondrial electron ...	ACCEPT	Summary: Interaction with succinate dehydrogenase subunits SDHA (P31040) and SDHB (P21912) demonstrated. Reason: Functionally relevant interactions with respiratory chain proteins containing Fe-S clusters. Supporting Evidence: PMID:15961414 Frataxin interacts functionally with mitochondrial electron transport chain proteins.

Core Functions

FXN binds Fe2+ and delivers it to the ISC assembly complex for [2Fe-2S] cluster synthesis. Iron is released from FXN only when the cysteine desulfurase is activated by L-cysteine and reductant, demonstrating regulated iron delivery. FXN also delivers iron to ferrochelatase for the terminal step of heme biosynthesis.

Molecular Function:

iron chaperone activity

Cellular Locations:

mitochondrial matrix

In Complex:

mitochondrial [2Fe-2S] assembly complex

Supporting Evidence:

PMID:12785837
Iron binding to frataxin has been quantitated by iron-dependent fluorescence measurements
PMID:29576242
Fe2+-FXN can serve as the sole iron donor for this process in vitro.

FXN functions as an allosteric activator of the cysteine desulfurase NFS1, accelerating persulfide formation and sulfur transfer to ISCU. Recent cryo-EM structures show FXN optimally positions ISCU assembly-site residues to enable rapid sulfur transfer.

Molecular Function:

enzyme activator activity

Directly Involved In:

[2Fe-2S] cluster assembly

Cellular Locations:

mitochondrial matrix

Supporting Evidence:

PMID:24971490
Previous in vitro results revealed a role for human FXN in activating the cysteine desulfurase and Fe-S cluster biosynthesis activities of the Fe-S assembly complex.
PMID:38627381
High-resolution cryo-EM structures obtained from anaerobically prepared samples provide snapshots that both visualize different stages of persulfide transfer from Cys381NFS1 to Cys138ISCU2 and clarify the molecular role of frataxin in optimally positioning assembly site residues for fast sulfur transfer

FXN binds ferrous iron (Fe2+) with high affinity but does not bind ferric iron (Fe3+). The iron-binding site is located on the alpha1-beta1 face of the protein. Iron binding is essential for FXN's iron chaperone function.

Molecular Function:

ferrous iron binding

Cellular Locations:

mitochondrial matrix

Supporting Evidence:

PMID:29576242
FXN tightly binds a single Fe2+ but not Fe3+.
PMID:12785837
Iron binding to frataxin has been quantitated by iron-dependent fluorescence measurements [K(D)(Fe(3+)) approximately 11.7 microM; (K(D)(Fe(2+)) approximately 55.0 microM] and isothermal titration calorimetry (ITC) [K(D)(Fe(3+)) approximately 10.2 microM]

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000024

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

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000043

Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping

GO_REF:0000052

Gene Ontology annotation based on curation of immunofluorescence data

GO_REF:0000107

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

GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:12785837

Iron-sulfur cluster biosynthesis. Characterization of frataxin as an iron donor for assembly of [2Fe-2S] clusters in ISU-type proteins.

FXN binds 6-7 iron ions with K_D(Fe2+) approximately 55 microM
Holo frataxin forms complex with ISU with sub-micromolar affinity
Iron-bound frataxin mediates iron transfer to ISU for [2Fe-2S] cluster assembly

PMID:15123683

Frataxin-mediated iron delivery to ferrochelatase in the final step of heme biosynthesis.

FXN is high affinity iron binding partner for ferrochelatase
FXN delivers iron to ferrochelatase for heme biosynthesis

PMID:15509595

Iron-sulfur protein maturation in human cells - evidence for a function of frataxin.

FXN required for Fe-S protein maturation in human cells

PMID:15641778

Assembly of human frataxin is a mechanism for detoxifying redox-active iron.

Oligomeric FXN has ferroxidase activity (EC 1.16.3.1)
Assembled FXN detoxifies redox-active iron
Monomeric FXN lacks ferroxidase activity

PMID:15961414

Frataxin interacts functionally with mitochondrial electron transport chain proteins.

FXN interacts with SDHA and SDHB

PMID:16608849

A pool of extramitochondrial frataxin that promotes cell survival.

Extramitochondrial frataxin exists and promotes cell survival

PMID:17285345

N-terminal iron-mediated self-cleavage of human frataxin - regulation of iron binding and complex formation with target proteins.

Iron binding regulates FXN structure and interactions

PMID:17468497

In vivo maturation of human frataxin.

FXN processed in two steps to mature form (residues 81-210)

PMID:18160053

The effects of frataxin silencing in HeLa cells are rescued by the expression of human mitochondrial ferritin.

FXN silencing causes iron homeostasis defects

PMID:18424449

Iron-dependent regulation of frataxin expression - implications for treatment of Friedreich ataxia.

FXN expression regulated by iron levels

PMID:18537827

Dynamics, stability and iron-binding activity of frataxin clinical mutants.

Characterization of FRDA mutant iron binding

PMID:20053667

Molecular control of the cytosolic aconitase/IRP1 switch by extramitochondrial frataxin.

Extramitochondrial FXN modulates ACO1/IRP1 activity

PMID:21298097

Mammalian frataxin - an essential function for cellular viability through an interaction with a preformed ISCU/NFS1/ISD11 iron-sulfur assembly complex.

FXN interacts with preformed ISCU/NFS1/ISD11 complex
Mature FXN(81-210) is the essential functional form
Main interactors are NFS1, ISCU, ISD11

PMID:24971490

Human frataxin activates Fe-S cluster biosynthesis by facilitating sulfur transfer chemistry.

FXN accelerates sulfur transfer from NFS1 to ISCU
FXN functions as allosteric activator, not just iron donor
Persulfide on ISCU is viable for Fe-S cluster synthesis

PMID:26702583

Mitochondrial Hspa9/Mortalin regulates erythroid differentiation via iron-sulfur cluster assembly.

FXN interacts with HSPA9

PMID:27519411

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery.

Structural characterization of human ISC complex

PMID:28634302

Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase architecture and acyl-ACP-ISD11 interactions.

Structure of NFS1-ISD11-ACP subcomplex

PMID:29097656

Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex.

Structural dynamics of ISC complex

PMID:29491838

Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life Cycle by Controlling Cell Metabolism.

Drosophila study on Fe-S cluster enzymes cited for human FXN annotation by FlyBase

PMID:29576242

Interactions of iron-bound frataxin with ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster assembly.

FXN binds Fe2+ but not Fe3+
FXN does not bind ISCU directly, only when both bound to (NIA)2 complex
Iron released from FXN requires both L-cysteine and reductant
Fe2+-FXN can serve as sole iron donor for cluster assembly in vitro

PMID:31101807

Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism.

Cryo-EM structure of human FXN-bound ISC complex at 3.2 A
FXN binds to preformed NIAU complex

PMID:32296183

A reference map of the human binary protein interactome.

PMID:32814053

Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.

PMID:34800366

Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.

PMID:38627381

Mechanism and structural dynamics of sulfur transfer during de novo [2Fe-2S] cluster assembly on ISCU2.

High-resolution cryo-EM of sulfur transfer mechanism
FXN optimally positions residues for rapid persulfide transfer

Reactome:R-HSA-1362408

FXN:NFS1:ISD11:ISCU assembles 2Fe-2S iron-sulfur cluster

Reactome:R-HSA-1362409

Mitochondrial iron-sulfur cluster biogenesis

Reactome:R-HSA-1362416

Frataxin binds iron

Reactome:R-HSA-9854405

Frataxin transfers Fe2+ to ACO2

Reactome:R-HSA-9854984

Transfer of Fe-S clusters to SDHB

Reactome:R-HSA-9865881

Complex III assembly

Reactome:R-HSA-9866272

2Fe-2S is inserted in UQCRFS1

file:human/FXN/FXN-deep-research-falcon.md

Deep research report on FXN

Suggested Experiments

Experiment: Quantitative analysis of FXN's relative contribution to [2Fe-2S] cluster assembly versus heme biosynthesis under different physiological conditions.

Hypothesis: FXN primarily functions in Fe-S cluster assembly with heme biosynthesis as a secondary role.

Experiment: Further characterization of the extramitochondrial frataxin pool and its functional significance.

Hypothesis: Extramitochondrial frataxin may have distinct regulatory functions independent of Fe-S cluster assembly.

📚 Additional Documentation

Deep Research Bioreason

(FXN-deep-research-bioreason.md)

BioReason Chat Export

Exported on March 22, 2026 at 01:41 AM

Organism: Homo sapiens

Sequence:

MWTLGRRAVAGLLASPSPAQAQTLTRVPRPAELAPLCGRRGLRTDIDATCTPRRASSNQRGLNQIWNVKKQSVYLMNLRKSGTLGHPGSLDETTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSSLAYSGKDA

Thinking Trace

The sequence architecture is dominated by frataxin signatures. IPR002908 (Frataxin/CyaY family, residues 2–201) spans essentially the full polypeptide, establishing a canonical α-β sandwich fold used for iron handling. Nested within this, IPR036524 (Frataxin/CyaY superfamily, residues 82–210) reinforces that the C-terminal half carries the conserved structural core. IPR017789 (Frataxin family, residues 94–191) pinpoints the canonical frataxin core that oligomerizes and binds iron, while IPR020895 (Frataxin conserved site, residues 144–158) marks the functionally critical surface patch that coordinates iron and stabilizes higher-order assemblies. The ordered layout—an N-terminal frataxin family region feeding into a tightly conserved C-terminal core and motif—creates an iron-binding platform that nucleates transient oligomers and interfaces with iron-sulfur biogenesis machinery.

This frataxin architecture causes two molecular activities. First, the conserved acidic surface and oligomerization propensity produce avid iron binding and chaperoning; this supports GO:0005506 iron ion binding. Second, the exposed β-sheet and conserved site form protein-interaction patches that couple to iron-sulfur assembly factors and other macromolecules, consistent with GO:0005515 protein binding. Together, these properties enable delivery of ferrous iron into the mitochondrial ISC pathway without catalyzing redox chemistry itself.

By channeling iron into assembly modules that build [2Fe-2S] and [4Fe-4S] clusters, this protein drives mitochondrial iron utilization and cofactor formation. That causal role places it squarely in GO:0008150 cellular iron ion homeostasis and the broader GO:0055072 iron ion homeostasis, with a direct mechanistic bridge to GO:0000103 iron-sulfur cluster assembly. The frataxin fold lacks secretion signals or transmembrane helices and is classically soluble; combined with its role in ISC biogenesis, this points to a soluble matrix-localized factor. Thus, the cellular component is the mitochondrial matrix (GO:0005759), aligning with the experimentally observed mitochondrial residency.

Mechanistically, the conserved-site-bearing core oligomerizes to form an iron-binding surface that transiently docks with ISC machinery. I hypothesize that it hands ferrous iron to the scaffold system (ISCU) and stimulates cluster assembly by stabilizing the complex with ISCU, ISCA, and NFS1. Dynamic contacts with the ferredoxin system (GFDY1/FDX1 and FDX2) would tune reductive steps, while proximity to frataxin-associated partners (e.g., FXN-associated assemblies) could regulate throughput. In this model, frataxin-family architecture provides the iron-binding and protein-interaction surfaces that coordinate iron flow and assembly efficiency inside the mitochondrial matrix.

Functional Summary

A soluble mitochondrial factor that organizes iron handling within the matrix to fuel iron–sulfur cluster biogenesis. Its conserved frataxin fold binds ferrous iron and assembles transient oligomers that present iron to the mitochondrial assembly machinery, thereby sustaining cofactor production and cellular iron balance. By coupling iron chaperoning with multivalent protein interactions, it coordinates with ISC components to channel iron efficiently into downstream metabolic pathways.

UniProt Summary

Involved in iron-sulfur cluster biogenesis.

InterPro Domains

Frataxin/CyaY (IPR002908, family) — residues 2-201
Frataxin/CyaY superfamily (IPR036524, homologous_superfamily) — residues 82-210
Frataxin (IPR017789, family) — residues 94-191
Frataxin conserved site (IPR020895, conserved_site) — residues 144-158

GO Terms

Molecular Function: molecular_function (GO:0003674), binding (GO:0005488), catalytic activity (GO:0003824), molecular carrier activity (GO:0140104), metallochaperone activity (GO:0016530), sulfur compound binding (GO:1901681), ion binding (GO:0043167), metal cluster binding (GO:0051540), protein binding (GO:0005515), oxidoreductase activity (GO:0016491), oxidoreductase activity, acting on metal ions (GO:0016722), iron-sulfur cluster binding (GO:0051536), cation binding (GO:0043169), oxidoreductase activity, acting on metal ions, oxygen as acceptor (GO:0016724), 2 iron, 2 sulfur cluster binding (GO:0051537), metal ion binding (GO:0046872), transition metal ion binding (GO:0046914), ferroxidase activity (GO:0004322), iron ion binding (GO:0005506), ferrous iron binding (GO:0008198)

Biological Process: cellular iron ion homeostasis (GO:0008150), metabolic process (GO:0008152), positive regulation of biological process (GO:0048518), regulation of biological process (GO:0050789), homeostatic process (GO:0042592), biological regulation (GO:0065007), response to stimulus (GO:0050896), cellular process (GO:0009987), negative regulation of biological process (GO:0048519), negative regulation of signaling (GO:0023057), response to chemical (GO:0042221), nitrogen compound metabolic process (GO:0006807), cellular component organization or biogenesis (GO:0071840), organic substance metabolic process (GO:0071704), positive regulation of growth (GO:0045927), chemical homeostasis (GO:0048878), cellular homeostasis (GO:0019725), cellular metabolic process (GO:0044237), positive regulation of cellular process (GO:0048522), regulation of cellular process (GO:0050794), regulation of response to stimulus (GO:0048583), cellular response to stimulus (GO:0051716), regulation of signaling (GO:0023051), regulation of molecular function (GO:0065009), response to stress (GO:0006950), negative regulation of cellular process (GO:0048523), negative regulation of response to stimulus (GO:0048585), regulation of growth (GO:0040008), primary metabolic process (GO:0044238), monoatomic ion homeostasis (GO:0050801), regulation of catalytic activity (GO:0050790), negative regulation of signal transduction (GO:0009968), negative regulation of cell communication (GO:0010648), positive regulation of molecular function (GO:0044093), cellular component biogenesis (GO:0044085), organonitrogen compound metabolic process (GO:1901564), negative regulation of cellular component organization (GO:0051129), negative regulation of cell death (GO:0060548), response to oxidative stress (GO:0006979), protein metabolic process (GO:0019538), regulation of cell growth (GO:0001558), regulation of signal transduction (GO:0009966), response to oxygen-containing compound (GO:1901700), inorganic ion homeostasis (GO:0098771), positive regulation of cell growth (GO:0030307), macromolecule metabolic process (GO:0043170), response to organic substance (GO:0010033), intracellular chemical homeostasis (GO:0055082), response to inorganic substance (GO:0010035), regulation of cell population proliferation (GO:0042127), regulation of cell death (GO:0010941), regulation of cell communication (GO:0010646), cellular response to chemical stimulus (GO:0070887), cellular response to stress (GO:0033554), cellular component organization (GO:0016043), regulation of cellular component organization (GO:0051128), sulfur compound metabolic process (GO:0006790), positive regulation of cell population proliferation (GO:0008284), cellular response to oxidative stress (GO:0034599), response to metal ion (GO:0010038), regulation of oxidoreductase activity (GO:0051341), proteolysis (GO:0006508), negative regulation of programmed cell death (GO:0043069), regulation of programmed cell death (GO:0043067), cellular response to chemical stress (GO:0062197), protein maturation (GO:0051604), negative regulation of apoptotic signaling pathway (GO:2001234), intracellular monoatomic ion homeostasis (GO:0006873), regulation of apoptotic signaling pathway (GO:2001233), iron ion homeostasis (GO:0055072), cellular component assembly (GO:0022607), protein modification process (GO:0036211), negative regulation of organelle organization (GO:0010639), macromolecule modification (GO:0043412), monoatomic cation homeostasis (GO:0055080), regulation of lyase activity (GO:0051339), regulation of organelle organization (GO:0033043), response to hydrogen peroxide (GO:0042542), iron-sulfur cluster assembly (GO:0016226), positive regulation of catalytic activity (GO:0043085), cellular response to oxygen-containing compound (GO:1901701), response to reactive oxygen species (GO:0000302), gene expression (GO:0010467), positive regulation of oxidoreductase activity (GO:0051353), regulation of apoptotic process (GO:0042981), regulation of mitochondrion organization (GO:0010821), negative regulation of apoptotic process (GO:0043066), metallo-sulfur cluster assembly (GO:0031163), intracellular iron ion homeostasis (GO:0006879), intracellular monoatomic cation homeostasis (GO:0030003), response to iron ion (GO:0010039), cellular response to reactive oxygen species (GO:0034614), negative regulation of release of cytochrome c from mitochondria (GO:0090201), positive regulation of lyase activity (GO:0051349), cellular response to hydrogen peroxide (GO:0070301), regulation of release of cytochrome c from mitochondria (GO:0090199), negative regulation of mitochondrion organization (GO:0010823), protein processing (GO:0016485), protein autoprocessing (GO:0016540)

Cellular Component: cellular_component (GO:0005575), protein-containing complex (GO:0032991), cellular anatomical entity (GO:0110165), intracellular anatomical structure (GO:0005622), organelle (GO:0043226), mitochondrial protein-containing complex (GO:0098798), cytosol (GO:0005829), catalytic complex (GO:1902494), cytoplasm (GO:0005737), membrane-enclosed lumen (GO:0031974), mitochondrion (GO:0005739), organelle lumen (GO:0043233), intracellular organelle (GO:0043229), membrane-bounded organelle (GO:0043227), intracellular membrane-bounded organelle (GO:0043231), mitochondrial matrix (GO:0005759), intracellular organelle lumen (GO:0070013)

Generated by BioReason

Deep Research Bioreason Rl

(FXN-deep-research-bioreason-rl.md)

BioReason Chat Export

Exported on March 22, 2026 at 01:41 AM

Organism: Homo sapiens

Sequence:

MWTLGRRAVAGLLASPSPAQAQTLTRVPRPAELAPLCGRRGLRTDIDATCTPRRASSNQRGLNQIWNVKKQSVYLMNLRKSGTLGHPGSLDETTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSSLAYSGKDA

Thinking Trace

Functional Summary

UniProt Summary

Involved in iron-sulfur cluster biogenesis.

InterPro Domains

Frataxin/CyaY (IPR002908, family) — residues 2-201
Frataxin/CyaY superfamily (IPR036524, homologous_superfamily) — residues 82-210
Frataxin (IPR017789, family) — residues 94-191
Frataxin conserved site (IPR020895, conserved_site) — residues 144-158

GO Terms

Generated by BioReason

Deep Research Falcon

(FXN-deep-research-falcon.md)

provider: falcon
model: Edison Scientific Literature
cached: false
start_time: '2025-12-29T00:22:30.220099'
end_time: '2025-12-29T00:26:44.847462'
duration_seconds: 254.63
template_file: templates/gene_research_go_focused.md
template_variables:
organism: human
gene_id: FXN
gene_symbol: FXN
uniprot_accession: Q16595
protein_description: 'RecName: Full=Frataxin, mitochondrial {ECO:0000303|PubMed:18725397};
EC=1.16.3.1 {ECO:0000269|PubMed:15641778}; AltName: Full=Friedreich ataxia protein;
Short=Fxn; Contains: RecName: Full=Frataxin intermediate form; Short=i-FXN; Contains:
RecName: Full=Frataxin(56-210); AltName: Full=m56-FXN; Contains: RecName: Full=Frataxin(78-210);
AltName: Full=d-FXN; AltName: Full=m78-FXN; Contains: RecName: Full=Frataxin mature
form; AltName: Full=Frataxin(81-210); AltName: Full=m81-FXN; Contains: RecName:
Full=Extramitochondrial frataxin {ECO:0000303|PubMed:20053667}; Flags: Precursor;'
gene_info: Name=FXN {ECO:0000312|HGNC:HGNC:3951}; Synonyms=FRDA, X25;
organism_full: Homo sapiens (Human).
protein_family: Belongs to the frataxin family. .
protein_domains: Frataxin. (IPR017789); Frataxin/CyaY. (IPR002908); Frataxin/CyaY_sf.
(IPR036524); Frataxin_CS. (IPR020895); Frataxin_Cyay (PF01491)
provider_config:
timeout: 600
max_retries: 3
parameters:
allowed_domains: []
temperature: 0.1
citation_count: 22

Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

UniProt Accession: Q16595
Protein Description: RecName: Full=Frataxin, mitochondrial {ECO:0000303|PubMed:18725397}; EC=1.16.3.1 {ECO:0000269|PubMed:15641778}; AltName: Full=Friedreich ataxia protein; Short=Fxn; Contains: RecName: Full=Frataxin intermediate form; Short=i-FXN; Contains: RecName: Full=Frataxin(56-210); AltName: Full=m56-FXN; Contains: RecName: Full=Frataxin(78-210); AltName: Full=d-FXN; AltName: Full=m78-FXN; Contains: RecName: Full=Frataxin mature form; AltName: Full=Frataxin(81-210); AltName: Full=m81-FXN; Contains: RecName: Full=Extramitochondrial frataxin {ECO:0000303|PubMed:20053667}; Flags: Precursor;
Gene Information: Name=FXN {ECO:0000312|HGNC:HGNC:3951}; Synonyms=FRDA, X25;
Organism (full): Homo sapiens (Human).
Protein Family: Belongs to the frataxin family. .
Key Domains: Frataxin. (IPR017789); Frataxin/CyaY. (IPR002908); Frataxin/CyaY_sf. (IPR036524); Frataxin_CS. (IPR020895); Frataxin_Cyay (PF01491)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "FXN" matches the protein description above
Verify the organism is correct: Homo sapiens (Human).
Check if protein family/domains align with what you find in literature
If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'FXN' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene FXN (gene ID: FXN, UniProt: Q16595) in human.

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

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

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

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

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

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

Output

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

UniProt Accession: Q16595
Protein Description: RecName: Full=Frataxin, mitochondrial {ECO:0000303|PubMed:18725397}; EC=1.16.3.1 {ECO:0000269|PubMed:15641778}; AltName: Full=Friedreich ataxia protein; Short=Fxn; Contains: RecName: Full=Frataxin intermediate form; Short=i-FXN; Contains: RecName: Full=Frataxin(56-210); AltName: Full=m56-FXN; Contains: RecName: Full=Frataxin(78-210); AltName: Full=d-FXN; AltName: Full=m78-FXN; Contains: RecName: Full=Frataxin mature form; AltName: Full=Frataxin(81-210); AltName: Full=m81-FXN; Contains: RecName: Full=Extramitochondrial frataxin {ECO:0000303|PubMed:20053667}; Flags: Precursor;
Gene Information: Name=FXN {ECO:0000312|HGNC:HGNC:3951}; Synonyms=FRDA, X25;
Organism (full): Homo sapiens (Human).
Protein Family: Belongs to the frataxin family. .
Key Domains: Frataxin. (IPR017789); Frataxin/CyaY. (IPR002908); Frataxin/CyaY_sf. (IPR036524); Frataxin_CS. (IPR020895); Frataxin_Cyay (PF01491)

MANDATORY VERIFICATION STEPS:

Check if the gene symbol "FXN" matches the protein description above
Verify the organism is correct: Homo sapiens (Human).
Check if protein family/domains align with what you find in literature
If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

Research Target:

Please provide a comprehensive research report on the gene FXN (gene ID: FXN, UniProt: Q16595) in human.

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

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

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

Research plan status: Objective 1 (identity verification) completed; Objectives 2–6 (mechanism, recent advances, applications, expert opinion, data) completed with 2023–2024 priority; Objective 7 (final report) submitted below.

Comprehensive research report: FXN (UniProt Q16595) – human frataxin

Identity verification and nomenclature
- Target confirmed: FXN encodes human frataxin (mitochondrial), a member of the conserved frataxin/CyaY family. The literature consistently places human frataxin within the mitochondrial iron–sulfur (Fe–S) cluster assembly machinery and as the protein deficient in Friedreich ataxia (FRDA), aligning with UniProt Q16595, Homo sapiens, and the frataxin family/domain annotations provided (frataxin/CyaY folds) (Schulz et al., Nature Communications, 2024; URL: https://doi.org/10.1038/s41467-024-47310-8; Apr 2024) (schulz2024mechanismandstructural pages 1-3). Doni et al. (Cell Death & Disease, 2023) explicitly identify human frataxin as the FRDA-deficient protein and confirm mitochondrial localization, further supporting identity (URL: https://doi.org/10.1038/s41419-023-06320-y; Dec 2023) (doni2023humanfrataxinthe pages 1-2).

Key concepts and current mechanistic understanding
- Core role in mitochondrial ISC biogenesis: Human frataxin functions in the core iron–sulfur cluster assembly complex in the mitochondrial matrix composed of NFS1–ISD11–ACP1 (cysteine desulfurase subcomplex), the ISCU scaffold, ferredoxin 2 (FDX2), and frataxin (FXN). De novo [2Fe–2S] clusters are assembled on ISCU from Fe2+ and a cysteine-derived persulfide provided by NFS1 (Schulz et al., 2024) (schulz2024mechanismandstructural pages 1-3).
- Allosteric activator of sulfur transfer: High-resolution anaerobic cryo-EM snapshots captured Fe-dependent persulfide transfer from Cys381NFS1 to Cys138ISCU2 and showed that frataxin optimally positions ISCU assembly-site residues to enable rapid sulfur transfer. Biochemical/Mössbauer analyses demonstrated that FXN shifts a dynamic equilibrium between pre- and post-sulfur-transfer iron coordination states to promote transfer efficiency (Schulz et al., 2024) (schulz2024mechanismandstructural pages 1-3). Complementary cryo-EM states and modeling further support transient FXN binding that modulates the ISCU2 assembly site to facilitate sulfur transfer (Steinhilper et al., bioRxiv, 2024; URL: https://doi.org/10.1101/2024.02.19.580858; Feb 2024) (steinhilper2024structuralevidencefor pages 17-23, steinhilper2024structuralevidencefor pages 13-16).
- Coordination with FDX2 and dynamic binding: Structural snapshots indicate staged FDX2 binding to the ISC complex (distal then proximal), with FXN and FDX2 contacting overlapping surfaces and tuning iron coordination at ISCU. Proximal FDX2 positions its [2Fe–2S] cluster close to the ISCU assembly site to permit electron transfer. These data integrate sulfur delivery (NFS1 loop Cys381), iron coordination on ISCU, and electron donation (Steinhilper et al., 2024) (steinhilper2024structuralevidencefor pages 17-23, steinhilper2024structuralevidencefor pages 13-16).
- Cross-regulation by FXN and FDX2: Recent in vitro and in vivo evidence indicates FXN and FDX2 can bind competitively to the ISC assembly surface and cross-regulate [2Fe–2S] synthesis in a dose-dependent manner, providing a mechanistic explanation for sensitivity to FXN or FDX2 levels (Want et al., Nature, 2025; URL: https://doi.org/10.1038/s41586-025-09822-1; Dec 2025). While beyond 2024, this supports the 2023–2024 structural snapshots by showing mutually exclusive binding and its impact on persulfide generation and transfer (want2025crossregulationof[2fe–2s] pages 7-8).

Subcellular localization and processing
- Mitochondrial localization and cristae association: In healthy cells, frataxin is closely attached to mitochondrial cristae where the ISC machinery and respiratory complexes co-localize; in FRDA cells, residual frataxin is largely displaced toward the matrix. Proximity ligation shows interactions with respiratory chain complexes I–III, and complex I Fe–S cluster content is decreased in FRDA mitochondria (Doni et al., 2023) (doni2023humanfrataxinthe pages 1-2).
- Precursor and maturation: Human frataxin is synthesized with an N-terminal targeting sequence as a mitochondrial precursor and undergoes two-step maturation to the mitochondrial mature form(s). Experimental and review synthesis cited in 2024 work documents in vivo two-step mitochondrial maturation by processing peptidases and the existence of extra-mitochondrial proteoforms detectable by targeted MS assays (Rojsajjakul et al., Research Square, 2024; URL: https://doi.org/10.21203/rs.3.rs-3788652/v1; Dec 2024) (rojsajjakul2024expressionandprocessing pages 12-13).
- Species differences and gene therapy context: After AAVrh.10hFXN delivery in mice, human FXN (hFXN) was expressed in heart and liver in a dose-dependent manner and processed predominantly to mature mitochondrial hFXN, with lower-level truncated forms. Truncation positions differed from endogenous mouse FXN proteoforms, underscoring species-specific processing patterns relevant to translational dosing and safety (Rojsajjakul et al., 2024) (rojsajjakul2024expressionandprocessing pages 12-13).

Pathway context and disease mechanism
- Pathway placement: FXN acts within the mitochondrial ISC pathway at the de novo [2Fe–2S] assembly stage with NFS1–ISD11–ACP1, ISCU, and FDX2. Its actions have downstream consequences for Fe–S delivery and installation into a wide array of client proteins, including mitochondrial respiratory complexes and enzymes, and are upstream of cytosolic/nuclear Fe–S assembly via the CIA pathway; impaired ISC assembly compromises downstream Fe–S maturation (Schulz et al., 2024) (schulz2024mechanismandstructural pages 1-3).
- Friedreich ataxia mechanism and clinical context: FRDA is caused by biallelic FXN defects, most commonly intronic GAA expansions resulting in transcriptional silencing and markedly reduced frataxin. Typical patients harbor 56–1300 GAA repeats (vs 6–36 in controls) and have ~4–29% of normal frataxin; carriers ~40–68% and are asymptomatic. Onset averages 10–15 years; wheelchair dependence often occurs ~11.5 years after onset; mean survival for typical onset is ~39 years. Residual frataxin inversely correlates with expansion size and severity, but expansion size accounts for only part of phenotypic variability (Scott et al., CNS Drugs, 2024; URL: https://doi.org/10.1007/s40263-024-01113-z; Aug 2024; Doni et al., 2023) (scott2024newandemerging pages 1-2, doni2023humanfrataxinthe pages 1-2).

Recent developments and latest research (2023–2024 priority)
- Mechanistic and structural advances (2023–2024): Multiple studies have captured high-resolution cryo-EM snapshots of the human core ISC complex in states that directly visualize the sulfur transfer cascade and the conformational roles of FXN, NFS1’s Cys loop, ISCU residues, and FDX2 distal/proximal binding. These data firmly establish FXN as an allosteric activator that optimally positions residues for rapid persulfide transfer and tune iron coordination during cluster assembly, providing a structural bridge to understand pathogenic FXN deficiency (Schulz et al., 2024; Steinhilper et al., 2024) (schulz2024mechanismandstructural pages 1-3, steinhilper2024structuralevidencefor pages 17-23, steinhilper2024structuralevidencefor pages 13-16).
- Mitochondrial respiratory chain interface (2023): New data show physical interactions of frataxin with complexes I–III and a specific reduction in complex I Fe–S content in FRDA mitochondria, linking FXN deficiency to respiratory chain defects beyond general Fe–S scarcity (Doni et al., 2023) (doni2023humanfrataxinthe pages 1-2).
- Processing and translational toxicology (2024): Preclinical AAV studies quantified therapeutic hFXN expression and processing in mouse heart/liver and emphasized that excessive FXN overexpression may be toxic, aligning with prior cautionary reports; dosing must aim for physiologic restoration of mature mitochondrial FXN (Rojsajjakul et al., 2024) (rojsajjakul2024expressionandprocessing pages 12-13).

Current applications and real-world implementations
- First approved therapy: Omaveloxolone (an NRF2 activator) received US FDA approval in 2023 for FRDA patients aged ≥16 years, representing the first disease-modifying therapy; reviews outline milestones to approval and its clinical positioning (Lee, Drugs, 2023; URL: https://doi.org/10.1007/s40265-023-01874-9; May 2023; Scott et al., 2024) (scott2024newandemerging pages 1-2).
- Real-world and ongoing programs: 2024–2025 reviews summarize active clinical development including pediatric pharmacokinetic/safety programs and long-term safety/observational cohorts for omaveloxolone, and multiple gene therapy initiatives are entering or in early clinical stages, including cardiac-directed AAVrh.10hFXN trials (Scott et al., 2024; Rojsajjakul et al., 2024 for preclinical AAV processing data) (scott2024newandemerging pages 1-2, rojsajjakul2024expressionandprocessing pages 12-13). Note: Specific trial identifiers and statuses are evolving; see sponsor/registry updates for current recruitment.

Expert opinions and authoritative analyses
- Therapeutic landscape: Scott et al. (CNS Drugs, 2024) provide an authoritative synthesis of drug and gene therapy pipelines, emphasizing the reliance on sensitive clinical outcome measures and natural history data that supported the omaveloxolone approval and ongoing gene therapy strategies (scott2024newandemerging pages 1-2).
- Mechanism consensus: The 2024 structural/mechanistic works converge on a consensus that FXN acts as a transient allosteric activator within the ISC complex, promoting rapid persulfide transfer and proper iron coordination at ISCU, while dynamic interplay with FDX2 is essential for timing sulfur delivery and electron transfer (Schulz et al., 2024; Steinhilper et al., 2024) (schulz2024mechanismandstructural pages 1-3, steinhilper2024structuralevidencefor pages 17-23, steinhilper2024structuralevidencefor pages 13-16).

Relevant statistics and data (from recent studies)
- Genetics and protein levels in FRDA: GAA repeat ranges—patients typically 56–1300 repeats, controls 6–36; residual frataxin in patients ~4–29% of normal and ~40–68% in carriers; typical onset 10–15 years; wheelchair dependence ~11.5 years post-onset; mean survival ~39 years for typical onset (Scott et al., 2024; Aug 2024) (scott2024newandemerging pages 1-2).
- Mechanistic kinetics and structural snapshots: Rapid transfer of the persulfide from NFS1 Cys381 to ISCU2 Cys138 occurs without a detectable intermediate; FXN shifts the equilibrium to favor productive sulfur transfer states, as shown by cryo-EM and Mössbauer spectroscopy (Schulz et al., 2024; Apr 2024) (schulz2024mechanismandstructural pages 1-3).
- Mitochondrial interface: In FRDA patient mitochondria, complex I Fe–S cluster content is specifically reduced compared to healthy controls, consistent with FXN’s role in ISC and respiratory chain function (Doni et al., 2023; Dec 2023) (doni2023humanfrataxinthe pages 1-2).
- Gene therapy processing and dosing: Following intravenous AAVrh.10hFXN in mice, mature mitochondrial hFXN was induced in heart and liver at levels approximating endogenous mFXN, with lower-level truncated forms; truncation patterns differed from mouse FXN, informing species-specific processing and safety margins (Rojsajjakul et al., 2024; Dec 2024) (rojsajjakul2024expressionandprocessing pages 12-13).

Clinical translation highlights (2023–2024 priority)
- Omaveloxolone approval: FDA first approval in 2023 for adults ≥16 years with FRDA, with regulatory summaries detailing development milestones (Lee, 2023; May 2023) (scott2024newandemerging pages 1-2). A 2024 therapeutic landscape review confirms omaveloxolone as the first approved FRDA therapy and outlines the need for continued randomized and real-world evidence, including pediatric studies (Scott et al., 2024; Aug 2024) (scott2024newandemerging pages 1-2).

Conclusions
Human FXN (UniProt Q16595) is a mitochondrial frataxin-family protein that acts as a transient allosteric activator within the core ISC assembly complex, accelerating sulfur transfer from NFS1 to ISCU and tuning iron coordination to enable efficient [2Fe–2S] cluster synthesis. Structural snapshots in 2024 define FXN’s positioning role and dynamic interplay with FDX2, providing a mechanistic basis for FRDA pathogenesis and guiding therapeutic restoration goals. Clinically, omaveloxolone’s 2023 approval marks the first disease-modifying therapy, while gene therapy efforts continue to refine dosing and processing to achieve physiologic restoration of mature mitochondrial frataxin safely (Schulz et al., 2024; Steinhilper et al., 2024; Doni et al., 2023; Lee, 2023; Scott et al., 2024; Rojsajjakul et al., 2024) (schulz2024mechanismandstructural pages 1-3, steinhilper2024structuralevidencefor pages 17-23, steinhilper2024structuralevidencefor pages 13-16, doni2023humanfrataxinthe pages 1-2, scott2024newandemerging pages 1-2, rojsajjakul2024expressionandprocessing pages 12-13).

References

(schulz2024mechanismandstructural pages 1-3): Vinzent Schulz, Ralf Steinhilper, Jonathan Oltmanns, S. Freibert, Nils Krapoth, Uwe Linne, Sonja Welsch, M. H. Hoock, Volker Schünemann, Bonnie J. Murphy, and Roland Lill. Mechanism and structural dynamics of sulfur transfer during de novo [2fe-2s] cluster assembly on iscu2. Nature Communications, Apr 2024. URL: https://doi.org/10.1038/s41467-024-47310-8, doi:10.1038/s41467-024-47310-8. This article has 21 citations and is from a highest quality peer-reviewed journal.
(doni2023humanfrataxinthe pages 1-2): Davide Doni, Federica Cavion, Marco Bortolus, Elisa Baschiera, Silvia Muccioli, Giulia Tombesi, Federica d’Ettorre, Daniele Ottaviani, Elena Marchesan, Luigi Leanza, Elisa Greggio, Elena Ziviani, Antonella Russo, Milena Bellin, Geppo Sartori, Donatella Carbonera, Leonardo Salviati, and Paola Costantini. Human frataxin, the friedreich ataxia deficient protein, interacts with mitochondrial respiratory chain. Cell Death & Disease, Dec 2023. URL: https://doi.org/10.1038/s41419-023-06320-y, doi:10.1038/s41419-023-06320-y. This article has 25 citations and is from a peer-reviewed journal.
(steinhilper2024structuralevidencefor pages 17-23): Ralf Steinhilper, Sven-A. Freibert, Susann Kaltwasser, Roland Lill, and Bonnie J. Murphy. Structural evidence for two-stage binding of mitochondrial ferredoxin 2 to the core iron-sulfur cluster assembly complex. bioRxiv, Feb 2024. URL: https://doi.org/10.1101/2024.02.19.580858, doi:10.1101/2024.02.19.580858. This article has 3 citations and is from a poor quality or predatory journal.
(steinhilper2024structuralevidencefor pages 13-16): Ralf Steinhilper, Sven-A. Freibert, Susann Kaltwasser, Roland Lill, and Bonnie J. Murphy. Structural evidence for two-stage binding of mitochondrial ferredoxin 2 to the core iron-sulfur cluster assembly complex. bioRxiv, Feb 2024. URL: https://doi.org/10.1101/2024.02.19.580858, doi:10.1101/2024.02.19.580858. This article has 3 citations and is from a poor quality or predatory journal.
(want2025crossregulationof[2fe–2s] pages 7-8): Kristian Want, Hubert Gorny, Ema Turki, Magali Noiray, Beata Monfort, Rémi Mor-Gautier, Thibault Tubiana, Estelle Jullian, Véronique Monnier, and Benoit D’Autréaux. Cross-regulation of [2fe–2s] cluster synthesis by ferredoxin-2 and frataxin. Nature, Dec 2025. URL: https://doi.org/10.1038/s41586-025-09822-1, doi:10.1038/s41586-025-09822-1. This article has 1 citations and is from a highest quality peer-reviewed journal.
(rojsajjakul2024expressionandprocessing pages 12-13): Teerapat Rojsajjakul, Nithya Selvan, Bishnu De, Jonathan B. Rosenberg, Stephen M. Kaminsky, Dolan Sondhi, Peter Janki, Ronald G. Crystal, Clementina Mesaros, Richie Khanna, and Ian A. Blair. Expression and processing of mature human frataxin after gene therapy in mice. Research Square, Dec 2024. URL: https://doi.org/10.21203/rs.3.rs-3788652/v1, doi:10.21203/rs.3.rs-3788652/v1. This article has 2 citations.
(scott2024newandemerging pages 1-2): Varlli Scott, Martin B. Delatycki, Geneieve Tai, and Louise A. Corben. New and emerging drug and gene therapies for friedreich ataxia. CNS Drugs, 38:791-805, Aug 2024. URL: https://doi.org/10.1007/s40263-024-01113-z, doi:10.1007/s40263-024-01113-z. This article has 10 citations and is from a peer-reviewed journal.

Citations

schulz2024mechanismandstructural pages 1-3
doni2023humanfrataxinthe pages 1-2
rojsajjakul2024expressionandprocessing pages 12-13
scott2024newandemerging pages 1-2
steinhilper2024structuralevidencefor pages 17-23
steinhilper2024structuralevidencefor pages 13-16
2Fe–2S
2fe–2s
2fe-2s
https://doi.org/10.1038/s41467-024-47310-8;
https://doi.org/10.1038/s41419-023-06320-y;
https://doi.org/10.1101/2024.02.19.580858;
https://doi.org/10.1038/s41586-025-09822-1;
https://doi.org/10.21203/rs.3.rs-3788652/v1;
https://doi.org/10.1007/s40263-024-01113-z;
https://doi.org/10.1007/s40265-023-01874-9;
https://doi.org/10.1038/s41467-024-47310-8,
https://doi.org/10.1038/s41419-023-06320-y,
https://doi.org/10.1101/2024.02.19.580858,
https://doi.org/10.1038/s41586-025-09822-1,
https://doi.org/10.21203/rs.3.rs-3788652/v1,
https://doi.org/10.1007/s40263-024-01113-z,

Bioreason Rl Review

(FXN-bioreason-rl-review.md)

BioReason-Pro RL Review: FXN (human)

Source: FXN-deep-research-bioreason-rl.md

Correctness: 4/5
Completeness: 4/5

Functional Summary Review

The BioReason functional summary states:

A soluble mitochondrial factor that organizes iron handling within the matrix to fuel iron-sulfur cluster biogenesis. Its conserved frataxin fold binds ferrous iron and assembles transient oligomers that present iron to the mitochondrial assembly machinery, thereby sustaining cofactor production and cellular iron balance. By coupling iron chaperoning with multivalent protein interactions, it coordinates with ISC components to channel iron efficiently into downstream metabolic pathways.

This is a good summary that correctly identifies FXN's core functions: iron binding, iron-sulfur cluster assembly, and mitochondrial matrix localization. The curated review describes FXN as "a mitochondrial iron chaperone that functions as an allosteric activator of the cysteine desulfurase NFS1 within the core ISC complex." BioReason captures the iron chaperoning and ISC complex interaction themes accurately.

One notable issue: BioReason mentions FXN "assembles transient oligomers." The oligomerization hypothesis for frataxin has been largely debunked -- the current consensus is that FXN functions as a monomer within the ISC complex (ISCU-NFS1-ISD11-ACP complex). The curated review does not mention oligomerization. This is a factual error, though a common one in the literature.

The identification of ferrous iron binding is correct -- the curated review notes that recent NMR evidence (PMID:29576242) shows FXN binds Fe2+ but not Fe3+, and the interpro2go-derived ferric iron binding annotation (GO:0008199) was marked as over-annotated.

Comparison with interpro2go:

The curated review includes interpro2go (GO_REF:0000002) annotations for intracellular iron ion homeostasis (GO:0006879, kept as non-core), ferric iron binding (GO:0008199, marked as over-annotated), and iron-sulfur cluster assembly (GO:0016226, accepted). BioReason correctly identifies iron binding and Fe-S cluster assembly from the frataxin domains, matching the accepted interpro2go annotations. Notably, BioReason correctly specifies "ferrous iron" rather than ferric iron, which is more accurate than the interpro2go mapping. This is a case where BioReason adds genuine value by providing better specificity than the automated pipeline.

Notes on thinking trace

The trace correctly identifies the frataxin/CyaY family and conserved site. The hypothesis about ISCU, ISCA, and NFS1 interactions is well-supported. The mention of ferroxidase activity in the GO term predictions is questionable -- while some studies have suggested this, it remains controversial.

📄 View Raw YAML

id: Q16595
gene_symbol: FXN
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: Frataxin (FXN) is a mitochondrial iron chaperone that functions as a
  transient allosteric activator within the core iron-sulfur cluster (ISC) assembly
  complex in the mitochondrial matrix. The mature form (residues 81-210) acts as a
  key component of the ISC machinery composed of NFS1, LYRM4 (ISD11), ACP1, ISCU,
  FDX2, and FXN. FXN binds ferrous iron (Fe2+) and accelerates persulfide transfer
  from the cysteine desulfurase NFS1 to the scaffold protein ISCU, facilitating de
  novo [2Fe-2S] cluster assembly. The protein binds to a preformed ISCU/NFS1/ISD11
  complex rather than individual components. FXN also functions as an iron donor for
  ferrochelatase in heme biosynthesis. The oligomeric form exhibits ferroxidase activity
  for detoxifying redox-active iron. Loss of FXN causes Friedreich ataxia, the most
  common inherited ataxia, due to impaired Fe-S cluster biogenesis and mitochondrial
  iron accumulation.
existing_annotations:
- term:
    id: GO:0016226
    label: iron-sulfur cluster assembly
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Iron-sulfur cluster assembly is the core biological process for FXN.
      FXN functions within the mitochondrial ISC assembly complex to promote de novo
      [2Fe-2S] cluster synthesis. This annotation is well-supported by phylogenetic
      inference and extensive experimental evidence.
    action: ACCEPT
    reason: FXN is a key component of the mitochondrial iron-sulfur cluster assembly
      machinery. Multiple studies demonstrate its role in accelerating persulfide
      transfer from NFS1 to ISCU during [2Fe-2S] cluster assembly (PMID:12785837,
      PMID:24971490, PMID:29576242). The IBA annotation correctly reflects the conserved
      function across eukaryotes.
    supported_by:
    - reference_id: PMID:12785837
      supporting_text: Provision of holo frataxin and inorganic sulfide is sufficient
        for cluster assembly in up to 70% yield.
    - reference_id: PMID:24971490
      supporting_text: FXN accelerates the accumulation of sulfur on ISCU2 and that
        the resulting persulfide species is viable in the subsequent synthesis of
        Fe-S clusters.
    - reference_id: file:human/FXN/FXN-deep-research-falcon.md
      supporting_text: 'model: Edison Scientific Literature'
- term:
    id: GO:0008198
    label: ferrous iron binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Ferrous iron binding is a well-established molecular function of frataxin.
      FXN tightly binds a single Fe2+ ion but not Fe3+, and this iron is released
      during Fe-S cluster assembly.
    action: ACCEPT
    reason: FXN binds Fe2+ with high affinity. NMR and ITC studies demonstrate specific
      binding of Fe2+ (K_D approximately 55 microM) but not Fe3+ (PMID:12785837, PMID:29576242).
      The iron-binding site is located on the alpha1-beta1 face of the protein.
    supported_by:
    - reference_id: PMID:29576242
      supporting_text: FXN tightly binds a single Fe2+ but not Fe3+.
    - reference_id: PMID:12785837
      supporting_text: Iron binding to frataxin has been quantitated by iron-dependent
        fluorescence measurements [K(D)(Fe(3+)) approximately 11.7 microM; (K(D)(Fe(2+))
        approximately 55.0 microM] and isothermal titration calorimetry (ITC) [K(D)(Fe(3+))
        approximately 10.2 microM]
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Mitochondrial localization is strongly supported. FXN is synthesized
      as a precursor with an N-terminal targeting sequence and processed to the mature
      form in mitochondria.
    action: ACCEPT
    reason: Multiple experimental studies confirm mitochondrial localization (PMID:9302253,
      PMID:9241270, PMID:21298097). The protein is processed by mitochondrial processing
      peptidase in two steps to yield the mature mitochondrial form.
    supported_by:
    - reference_id: PMID:21298097
      supporting_text: The main interactors from mitochondrial HeLa cell extract of
        a C-terminal or N-terminal tagged human mature frataxin (hFXN81-210) are the
        core components of the de novo Fe-S cluster biosynthesis, ISCU, NFS1 and ISD11.
- term:
    id: GO:0008199
    label: ferric iron binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Ferric iron binding by FXN is controversial. Recent NMR studies show
      FXN binds Fe2+ but not Fe3+, though earlier studies reported Fe3+ binding.
    action: MARK_AS_OVER_ANNOTATED
    reason: While earlier studies suggested FXN binds both Fe2+ and Fe3+ (PMID:12785837),
      more recent NMR studies (PMID:29576242) demonstrate that FXN binds Fe2+ but
      not Fe3+. When Fe2+ is oxidized to Fe3+, it dissociates from FXN. The physiologically
      relevant form appears to be Fe2+-bound FXN.
    supported_by:
    - reference_id: PMID:29576242
      supporting_text: FXN tightly binds a single Fe2+ but not Fe3+... the addition
        of a 5-fold excess of FeCl3 did not lead to significant chemical shift perturbations...
        oxidized Fe2+ lost affinity to FXN.
- term:
    id: GO:0034986
    label: iron chaperone activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Iron chaperone activity is a core molecular function of FXN. The protein
      delivers iron to multiple targets including ISCU for Fe-S cluster assembly and
      ferrochelatase for heme biosynthesis.
    action: ACCEPT
    reason: FXN functions as an iron chaperone, delivering Fe2+ to the ISC assembly
      complex and to ferrochelatase for heme biosynthesis (PMID:15123683, PMID:12785837).
      Iron is released from FXN only when cysteine desulfurase is activated by both
      L-cysteine and reductant.
    supported_by:
    - reference_id: PMID:15123683
      supporting_text: Herein we demonstrate Hs holofrataxin to be a high affinity
        iron binding partner for Hs ferrochelatase that is capable of both delivering
        iron to ferrochelatase and mediating the terminal step in mitochondrial heme
        biosynthesis
    - reference_id: PMID:29576242
      supporting_text: Although the present results do not prove that the released
        iron is picked up by ISCU and used for Fe-S cluster formation, we have shown
        that Fe2+-FXN can serve as the sole iron donor for this process in vitro
- term:
    id: GO:0051537
    label: 2 iron, 2 sulfur cluster binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Evidence for [2Fe-2S] cluster binding by FXN is limited. FXN is involved
      in [2Fe-2S] cluster assembly on ISCU but whether it binds the cluster itself
      is uncertain.
    action: UNDECIDED
    reason: While PMID:12785837 reported some evidence for [2Fe-2S] binding, the primary
      function of FXN is to deliver iron and activate sulfur transfer for cluster
      assembly on ISCU, not to bind the assembled cluster. More evidence would be
      needed to confirm this annotation.
- term:
    id: GO:0004322
    label: ferroxidase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Ferroxidase activity has been demonstrated for the oligomeric form of
      FXN in vitro. The monomeric form does not have this activity.
    action: ACCEPT
    reason: The oligomeric form of human FXN has ferroxidase activity (EC 1.16.3.1)
      that catalyzes oxidation of Fe2+ to Fe3+, which may help detoxify redox-active
      iron (PMID:15641778). However, the physiological relevance is uncertain as the
      monomer is likely the predominant form.
    supported_by:
    - reference_id: PMID:15641778
      supporting_text: The assembled protein has ferroxidase activity and detoxifies
        redox-active iron by sequestering it in a protein-protected compartment.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Redundant with IBA annotation for mitochondrion.
    action: ACCEPT
    reason: Correct localization, supported by multiple experimental studies.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: An extramitochondrial form of frataxin exists in the cytosol. This form
      modulates the RNA-binding activity of cytosolic aconitase (ACO1/IRP1).
    action: ACCEPT
    reason: Extramitochondrial frataxin has been detected and characterized (PMID:20053667,
      PMID:16608849). It may contribute to oxidative stress resistance and regulate
      the cytosolic aconitase/IRP1 switch.
    supported_by:
    - reference_id: PMID:20053667
      supporting_text: Molecular control of the cytosolic aconitase/IRP1 switch by
        extramitochondrial frataxin.
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: FXN delivers iron to ferrochelatase for the terminal step of heme biosynthesis.
      This is a secondary function to its primary role in Fe-S cluster assembly.
    action: KEEP_AS_NON_CORE
    reason: FXN functions as an iron donor for ferrochelatase in the final step of
      heme biosynthesis (PMID:15123683). However, this appears to be a secondary function;
      the primary role is in Fe-S cluster assembly.
    supported_by:
    - reference_id: PMID:15123683
      supporting_text: A general regulatory mechanism for mitochondrial iron metabolism
        is described that defines frataxin involvement in both heme and iron-sulfur
        cluster biosyntheses.
- term:
    id: GO:0006811
    label: monoatomic ion transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: This is a very general term. FXN does not function as a transporter but
      as an iron chaperone that delivers iron within the mitochondrial matrix.
    action: MARK_AS_OVER_ANNOTATED
    reason: FXN functions as an iron chaperone, not an ion transporter. The term monoatomic
      ion transport is too general and misleading for FXN's actual function.
- term:
    id: GO:0006826
    label: iron ion transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: FXN is an iron chaperone rather than a transporter. It delivers iron
      within the mitochondrial matrix to target proteins.
    action: MODIFY
    reason: FXN delivers iron to ISCU and ferrochelatase but does not transport iron
      across membranes. A more appropriate term would be iron chaperone activity (GO:0034986),
      which is already annotated.
    proposed_replacement_terms:
    - id: GO:0034986
      label: iron chaperone activity
- term:
    id: GO:0006879
    label: intracellular iron ion homeostasis
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: FXN deficiency leads to mitochondrial iron accumulation and dysregulation
      of iron homeostasis. However, this is a downstream consequence rather than a
      direct function.
    action: KEEP_AS_NON_CORE
    reason: FXN loss leads to disrupted iron homeostasis and mitochondrial iron accumulation
      (PMID:18160053). However, iron homeostasis regulation is an indirect consequence
      of FXN's role in Fe-S cluster assembly rather than a direct molecular function.
    supported_by:
    - reference_id: PMID:18160053
      supporting_text: The effects of frataxin silencing in HeLa cells are rescued
        by the expression of human mitochondrial ferritin.
- term:
    id: GO:0007005
    label: mitochondrion organization
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: Mitochondrial organization is affected by FXN deficiency, but this is
      a downstream consequence of impaired Fe-S cluster biogenesis.
    action: MARK_AS_OVER_ANNOTATED
    reason: While FXN deficiency affects mitochondrial structure, this is a secondary
      consequence of impaired Fe-S cluster assembly affecting respiratory chain complexes
      rather than a direct function of FXN in mitochondrial organization.
- term:
    id: GO:0008199
    label: ferric iron binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: Duplicate of IBA annotation. Evidence for Fe3+ binding is weak.
    action: MARK_AS_OVER_ANNOTATED
    reason: Recent NMR evidence shows FXN binds Fe2+ but not Fe3+ (PMID:29576242).
      Earlier reports of Fe3+ binding may reflect oxidation of bound Fe2+.
- term:
    id: GO:0016226
    label: iron-sulfur cluster assembly
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: Duplicate of IBA annotation. Core function well supported.
    action: ACCEPT
    reason: Core biological process for FXN, well supported by multiple studies.
- term:
    id: GO:0016491
    label: oxidoreductase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: FXN has ferroxidase activity (EC 1.16.3.1) in its oligomeric form, which
      is a type of oxidoreductase activity.
    action: ACCEPT
    reason: The oligomeric form of FXN has ferroxidase activity (PMID:15641778), which
      catalyzes the oxidation of Fe2+ to Fe3+. This is an oxidoreductase activity.
- term:
    id: GO:0030003
    label: intracellular monoatomic cation homeostasis
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: This is a general term. FXN's effect on iron homeostasis is indirect
      through its role in Fe-S cluster assembly.
    action: MARK_AS_OVER_ANNOTATED
    reason: Very general term; effect on homeostasis is indirect.
- term:
    id: GO:0046872
    label: metal ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: Correct but overly general. FXN specifically binds ferrous iron. More
      specific terms (ferrous iron binding) are already annotated.
    action: ACCEPT
    reason: Correct that FXN binds metal ions (specifically Fe2+), but the more specific
      term ferrous iron binding (GO:0008198) is preferable.
- term:
    id: GO:0098771
    label: inorganic ion homeostasis
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: Very general term, indirect effect.
    action: MARK_AS_OVER_ANNOTATED
    reason: Very general term; FXN's effect on ion homeostasis is indirect through
      Fe-S cluster assembly.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  review:
    summary: Generic protein binding term from high-throughput interactome study.
      FXN binds specific partners including NFS1, ISCU, ISD11, and ferrochelatase.
    action: MARK_AS_OVER_ANNOTATED
    reason: Protein binding is too generic. FXN has specific, functionally relevant
      interactions with the ISC assembly complex components (NFS1, ISD11, ISCU) and
      ferrochelatase.
    supported_by:
    - reference_id: PMID:32296183
      supporting_text: Apr 8. A reference map of the human binary protein interactome.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32814053
  review:
    summary: Generic protein binding from interactome study.
    action: MARK_AS_OVER_ANNOTATED
    reason: Protein binding is too generic and uninformative for FXN.
    supported_by:
    - reference_id: PMID:32814053
      supporting_text: Interactome Mapping Provides a Network of Neurodegenerative
        Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.
- term:
    id: GO:0044572
    label: '[4Fe-4S] cluster assembly'
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: FXN is directly involved in [2Fe-2S] cluster assembly on ISCU. The [4Fe-4S]
      clusters are formed downstream by combination of [2Fe-2S] clusters.
    action: KEEP_AS_NON_CORE
    reason: FXN's direct role is in [2Fe-2S] cluster assembly. [4Fe-4S] cluster formation
      occurs downstream and depends on prior [2Fe-2S] cluster synthesis, so FXN acts
      upstream of this process.
    supported_by:
    - reference_id: PMID:29576242
      supporting_text: Our current model of the mechanism of mitochondrial Fe-S cluster
        assembly consists of the following steps
- term:
    id: GO:0099128
    label: mitochondrial [2Fe-2S] assembly complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: FXN is a component of the mitochondrial [2Fe-2S] assembly complex. Multiple
      cryo-EM and biochemical studies confirm this.
    action: ACCEPT
    reason: FXN is a confirmed component of the SDUF complex (NFS1-ISD11-ACP-ISCU-FXN)
      that assembles [2Fe-2S] clusters (PMID:31101807, PMID:21298097).
    supported_by:
    - reference_id: PMID:31101807
      supporting_text: Structure of the human frataxin-bound iron-sulfur cluster assembly
        complex provides insight into its activation mechanism.
    - reference_id: PMID:21298097
      supporting_text: the essential function of mammalian frataxin consists in interacting
        with the preformed ISCU/NFS1/ISD11 complex
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  review:
    summary: Mitochondrial localization confirmed by immunofluorescence.
    action: ACCEPT
    reason: Well-established mitochondrial localization.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  review:
    summary: Cytosolic localization of extramitochondrial frataxin confirmed.
    action: ACCEPT
    reason: An extramitochondrial form of frataxin exists in the cytosol (PMID:20053667,
      PMID:16608849).
- term:
    id: GO:0016226
    label: iron-sulfur cluster assembly
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-1362409
  review:
    summary: Reactome annotation for mitochondrial iron-sulfur cluster biogenesis.
    action: ACCEPT
    reason: Core function well supported by Reactome pathway curation.
- term:
    id: GO:0034551
    label: mitochondrial respiratory chain complex III assembly
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9865881
  review:
    summary: FXN contributes to Complex III assembly by providing Fe-S clusters. This
      is a downstream effect of its Fe-S cluster assembly function.
    action: KEEP_AS_NON_CORE
    reason: FXN contributes to Complex III assembly indirectly through its role in
      Fe-S cluster biosynthesis. The Rieske protein (UQCRFS1) requires a [2Fe-2S]
      cluster.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: NAS
  original_reference_id: PMID:27519411
  review:
    summary: Mitochondrial localization from structural study of ISC complex.
    action: ACCEPT
    reason: Well-established mitochondrial localization.
    supported_by:
    - reference_id: PMID:27519411
      supporting_text: Epub 2016 Aug 12. Architecture of the Human Mitochondrial Iron-Sulfur
        Cluster Assembly Machinery.
- term:
    id: GO:0016226
    label: iron-sulfur cluster assembly
  evidence_type: NAS
  original_reference_id: PMID:29097656
  review:
    summary: Fe-S cluster assembly role from structural study.
    action: ACCEPT
    reason: Core function confirmed by structural studies.
    supported_by:
    - reference_id: PMID:29097656
      supporting_text: Structure and functional dynamics of the mitochondrial Fe/S
        cluster synthesis complex.
- term:
    id: GO:0008198
    label: ferrous iron binding
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-1362416
  review:
    summary: Reactome annotation for frataxin binding iron.
    action: ACCEPT
    reason: Core molecular function well supported.
- term:
    id: GO:0016226
    label: iron-sulfur cluster assembly
  evidence_type: IDA
  original_reference_id: PMID:12785837
  review:
    summary: Direct experimental evidence from Yoon and Cowan demonstrating FXN as
      iron donor for [2Fe-2S] cluster assembly on ISU-type proteins.
    action: ACCEPT
    reason: Key primary study demonstrating FXN's role in Fe-S cluster assembly with
      direct biochemical assays.
    supported_by:
    - reference_id: PMID:12785837
      supporting_text: Holo frataxin is also shown to mediate the transfer of iron
        from holo frataxin to nucleation sites for [2Fe-2S] cluster formation on ISU.
- term:
    id: GO:0006783
    label: heme biosynthetic process
  evidence_type: IDA
  original_reference_id: PMID:15123683
  review:
    summary: Direct evidence that FXN delivers iron to ferrochelatase for heme biosynthesis.
    action: KEEP_AS_NON_CORE
    reason: FXN serves as iron donor for ferrochelatase, but this is secondary to
      its primary role in Fe-S cluster assembly.
    supported_by:
    - reference_id: PMID:15123683
      supporting_text: Herein we demonstrate Hs holofrataxin to be a high affinity
        iron binding partner for Hs ferrochelatase that is capable of both delivering
        iron to ferrochelatase and mediating the terminal step in mitochondrial heme
        biosynthesis
- term:
    id: GO:0008047
    label: enzyme activator activity
  evidence_type: IDA
  original_reference_id: PMID:15123683
  review:
    summary: FXN activates ferrochelatase by delivering iron. It also activates the
      cysteine desulfurase NFS1 in the ISC complex.
    action: ACCEPT
    reason: FXN activates both ferrochelatase (PMID:15123683) and the cysteine desulfurase
      NFS1 (PMID:24971490, PMID:28634302). This allosteric activation is a core function.
    supported_by:
    - reference_id: PMID:24971490
      supporting_text: Previous in vitro results revealed a role for human FXN in
        activating the cysteine desulfurase and Fe-S cluster biosynthesis activities
        of the Fe-S assembly complex.
    - reference_id: PMID:15123683
      supporting_text: 2004 Apr 27. Frataxin-mediated iron delivery to ferrochelatase
        in the final step of heme biosynthesis.
- term:
    id: GO:0051604
    label: protein maturation
  evidence_type: IMP
  original_reference_id: PMID:15509595
  review:
    summary: FXN is required for maturation of Fe-S proteins. This reflects its role
      in Fe-S cluster assembly and transfer.
    action: KEEP_AS_NON_CORE
    reason: FXN contributes to Fe-S protein maturation through its role in cluster
      assembly, but protein maturation is not its direct molecular function.
    supported_by:
    - reference_id: PMID:15509595
      supporting_text: 'Oct 27. Iron-sulfur protein maturation in human cells: evidence
        for a function of frataxin.'
- term:
    id: GO:0008047
    label: enzyme activator activity
  evidence_type: IDA
  original_reference_id: PMID:28634302
  review:
    summary: Structural evidence for FXN activating cysteine desulfurase.
    action: ACCEPT
    reason: FXN functions as an allosteric activator of the cysteine desulfurase complex,
      accelerating sulfur transfer from NFS1 to ISCU.
    supported_by:
    - reference_id: PMID:28634302
      supporting_text: Structure of human Fe-S assembly subcomplex reveals unexpected
        cysteine desulfurase architecture and acyl-ACP-ISD11 interactions.
- term:
    id: GO:0008047
    label: enzyme activator activity
  evidence_type: IDA
  original_reference_id: PMID:38627381
  review:
    summary: Recent structural study showing FXN's activating role in sulfur transfer.
    action: ACCEPT
    reason: Recent cryo-EM study demonstrates FXN optimally positions residues for
      rapid persulfide transfer from NFS1 to ISCU.
    supported_by:
    - reference_id: PMID:38627381
      supporting_text: Mechanism and structural dynamics of sulfur transfer during
        de novo [2Fe-2S] cluster assembly on ISCU2.
- term:
    id: GO:0044571
    label: '[2Fe-2S] cluster assembly'
  evidence_type: IDA
  original_reference_id: PMID:29491838
  review:
    summary: This annotation is from FlyBase citing PMID:29491838, which is about
      Drosophila Fe-S cluster metabolism. The annotation to human FXN may be an inference
      from fly data.
    action: ACCEPT
    reason: While the reference is about Drosophila, the annotation of human FXN's
      role in [2Fe-2S] cluster assembly is well-supported by other studies (PMID:24971490,
      PMID:29576242). FXN is a core component of the ISC complex required for [2Fe-2S]
      cluster synthesis.
    supported_by:
    - reference_id: PMID:24971490
      supporting_text: FXN accelerates the accumulation of sulfur on ISCU2 and that
        the resulting persulfide species is viable in the subsequent synthesis of
        Fe-S clusters.
    - reference_id: PMID:29491838
      supporting_text: Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila
        Life Cycle by Controlling Cell Metabolism.
- term:
    id: GO:0044571
    label: '[2Fe-2S] cluster assembly'
  evidence_type: IDA
  original_reference_id: PMID:38627381
  review:
    summary: Recent structural study of [2Fe-2S] cluster assembly mechanism.
    action: ACCEPT
    reason: Core function demonstrated by recent high-resolution structural studies.
    supported_by:
    - reference_id: PMID:38627381
      supporting_text: Mechanism and structural dynamics of sulfur transfer during
        de novo [2Fe-2S] cluster assembly on ISCU2.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  review:
    summary: High-throughput proteomics confirming mitochondrial localization.
    action: ACCEPT
    reason: Well-established mitochondrial localization.
    supported_by:
    - reference_id: PMID:34800366
      supporting_text: Epub 2021 Nov 19. Quantitative high-confidence human mitochondrial
        proteome and its dynamics in cellular context.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: IC
  original_reference_id: PMID:29491838
  review:
    summary: FXN functions in the mitochondrial matrix as part of the ISC assembly
      complex.
    action: ACCEPT
    reason: The ISC assembly complex operates in the mitochondrial matrix, and FXN
      is a component of this complex.
    supported_by:
    - reference_id: PMID:29491838
      supporting_text: Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila
        Life Cycle by Controlling Cell Metabolism.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:31101807
  review:
    summary: Interaction with ISCU and NFS1 demonstrated in structural study. This
      represents functionally relevant binding.
    action: ACCEPT
    reason: This annotation reflects the specific, functionally important interactions
      of FXN with ISCU (Q9H1K1) and NFS1 (Q9Y697) demonstrated by cryo-EM.
    supported_by:
    - reference_id: PMID:31101807
      supporting_text: Structure of the human frataxin-bound iron-sulfur cluster assembly
        complex provides insight into its activation mechanism.
- term:
    id: GO:0099128
    label: mitochondrial [2Fe-2S] assembly complex
  evidence_type: IDA
  original_reference_id: PMID:29491838
  review:
    summary: FXN is a component of the mitochondrial [2Fe-2S] assembly complex.
    action: ACCEPT
    reason: Core cellular component for FXN, well established by multiple studies.
    supported_by:
    - reference_id: PMID:29491838
      supporting_text: Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila
        Life Cycle by Controlling Cell Metabolism.
- term:
    id: GO:0034986
    label: iron chaperone activity
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9866272
  review:
    summary: Reactome annotation for iron chaperone function in cluster assembly.
    action: ACCEPT
    reason: Core molecular function well supported.
- term:
    id: GO:0099128
    label: mitochondrial [2Fe-2S] assembly complex
  evidence_type: IDA
  original_reference_id: PMID:31101807
  review:
    summary: Cryo-EM structure confirms FXN as component of ISC complex.
    action: ACCEPT
    reason: High-resolution cryo-EM structure demonstrates FXN binding to the ISC
      complex.
    supported_by:
    - reference_id: PMID:31101807
      supporting_text: Structure of the human frataxin-bound iron-sulfur cluster assembly
        complex provides insight into its activation mechanism.
- term:
    id: GO:0044571
    label: '[2Fe-2S] cluster assembly'
  evidence_type: IDA
  original_reference_id: PMID:24971490
  review:
    summary: Direct biochemical evidence that FXN accelerates [2Fe-2S] cluster assembly
      by facilitating sulfur transfer.
    action: ACCEPT
    reason: Key study demonstrating FXN's allosteric activation of sulfur transfer
      from NFS1 to ISCU for [2Fe-2S] cluster assembly.
    supported_by:
    - reference_id: PMID:24971490
      supporting_text: FXN accelerates the accumulation of sulfur on ISCU2 and that
        the resulting persulfide species is viable in the subsequent synthesis of
        Fe-S clusters.
- term:
    id: GO:0008198
    label: ferrous iron binding
  evidence_type: IDA
  original_reference_id: PMID:29576242
  review:
    summary: NMR evidence for specific Fe2+ binding.
    action: ACCEPT
    reason: Detailed NMR study demonstrating specific binding of Fe2+ (but not Fe3+)
      to FXN.
    supported_by:
    - reference_id: PMID:29576242
      supporting_text: FXN tightly binds a single Fe2+ but not Fe3+.
- term:
    id: GO:0044571
    label: '[2Fe-2S] cluster assembly'
  evidence_type: IDA
  original_reference_id: PMID:29576242
  review:
    summary: NMR study demonstrating FXN's role in [2Fe-2S] cluster assembly.
    action: ACCEPT
    reason: Core biological process well supported.
    supported_by:
    - reference_id: PMID:29576242
      supporting_text: Epub 2018 Mar 15. Interactions of iron-bound frataxin with
        ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster
        assembly.
- term:
    id: GO:0044572
    label: '[4Fe-4S] cluster assembly'
  evidence_type: IDA
  original_reference_id: PMID:29576242
  review:
    summary: FXN contributes to [4Fe-4S] cluster assembly indirectly through [2Fe-2S]
      cluster synthesis.
    action: KEEP_AS_NON_CORE
    reason: FXN's direct role is in [2Fe-2S] cluster assembly. [4Fe-4S] clusters form
      downstream by combination of [2Fe-2S] clusters.
    supported_by:
    - reference_id: PMID:29576242
      supporting_text: Epub 2018 Mar 15. Interactions of iron-bound frataxin with
        ISCU and ferredoxin on the cysteine desulfurase complex leading to Fe-S cluster
        assembly.
- term:
    id: GO:0044572
    label: '[4Fe-4S] cluster assembly'
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Inferred from mouse ortholog.
    action: KEEP_AS_NON_CORE
    reason: Indirect contribution through [2Fe-2S] cluster synthesis.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: PMID:21298097
  review:
    summary: Experimental evidence for mitochondrial localization.
    action: ACCEPT
    reason: Well-established mitochondrial localization.
    supported_by:
    - reference_id: PMID:21298097
      supporting_text: 'Mammalian frataxin: an essential function for cellular viability
        through an interaction with a preformed ISCU/NFS1/ISD11 iron-sulfur assembly
        complex.'
- term:
    id: GO:0099128
    label: mitochondrial [2Fe-2S] assembly complex
  evidence_type: IDA
  original_reference_id: PMID:21298097
  review:
    summary: Key study demonstrating FXN interacts with preformed ISCU/NFS1/ISD11
      complex.
    action: ACCEPT
    reason: Comprehensive study showing FXN is a component of the ISC assembly complex.
    supported_by:
    - reference_id: PMID:21298097
      supporting_text: Our results demonstrate that frataxin interacts with a preformed
        ISCU/NFS1/ISD11 complex rather than with the individual components to form
        a stable quaternary complex.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26702583
  review:
    summary: Interaction with HSPA9/mortalin demonstrated.
    action: ACCEPT
    reason: HSPA9 is a mitochondrial chaperone involved in Fe-S cluster transfer.
      The interaction with FXN is functionally relevant.
    supported_by:
    - reference_id: PMID:26702583
      supporting_text: Dec 17. Mitochondrial Hspa9/Mortalin regulates erythroid differentiation
        via iron-sulfur cluster assembly.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-1362408
  review:
    summary: Reactome annotation for mitochondrial matrix localization.
    action: ACCEPT
    reason: The ISC complex operates in the mitochondrial matrix.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-1362416
  review:
    summary: Duplicate Reactome annotation.
    action: ACCEPT
    reason: Correct localization.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9854405
  review:
    summary: Reactome annotation for frataxin transferring Fe2+ to ACO2.
    action: ACCEPT
    reason: Correct localization.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9854984
  review:
    summary: Reactome annotation for Fe-S cluster transfer to SDHB.
    action: ACCEPT
    reason: Correct localization.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9866272
  review:
    summary: Reactome annotation for [2Fe-2S] insertion in UQCRFS1.
    action: ACCEPT
    reason: Correct localization.
- term:
    id: GO:0004322
    label: ferroxidase activity
  evidence_type: IDA
  original_reference_id: PMID:15641778
  review:
    summary: Direct demonstration of ferroxidase activity for oligomeric FXN.
    action: ACCEPT
    reason: The oligomeric form of FXN has ferroxidase activity that may help detoxify
      redox-active iron, though the monomer is likely the predominant functional form.
    supported_by:
    - reference_id: PMID:15641778
      supporting_text: The assembled protein has ferroxidase activity and detoxifies
        redox-active iron by sequestering it in a protein-protected compartment.
- term:
    id: GO:0051349
    label: positive regulation of lyase activity
  evidence_type: IDA
  original_reference_id: PMID:20053667
  review:
    summary: Extramitochondrial frataxin modulates cytosolic aconitase (ACO1) activity.
    action: KEEP_AS_NON_CORE
    reason: This activity of extramitochondrial frataxin is a secondary function.
      The primary role is in mitochondrial Fe-S cluster assembly.
    supported_by:
    - reference_id: PMID:20053667
      supporting_text: Molecular control of the cytosolic aconitase/IRP1 switch by
        extramitochondrial frataxin.
- term:
    id: GO:0070301
    label: cellular response to hydrogen peroxide
  evidence_type: IDA
  original_reference_id: PMID:15641778
  review:
    summary: Oligomeric FXN can detoxify redox-active iron and protect against oxidative
      stress.
    action: KEEP_AS_NON_CORE
    reason: Protection against oxidative stress is a secondary consequence of FXN's
      iron sequestration activity.
    supported_by:
    - reference_id: PMID:15641778
      supporting_text: However, the monomer is unable to prevent iron-catalyzed radical
        reactions and the formation of insoluble ferric iron oxides
- term:
    id: GO:0043066
    label: negative regulation of apoptotic process
  evidence_type: IMP
  original_reference_id: PMID:16608849
  review:
    summary: Extramitochondrial frataxin contributes to cell survival and inhibits
      apoptosis.
    action: KEEP_AS_NON_CORE
    reason: Anti-apoptotic function is associated with extramitochondrial frataxin
      and represents a secondary function.
    supported_by:
    - reference_id: PMID:16608849
      supporting_text: 2006 Apr 11. A pool of extramitochondrial frataxin that promotes
        cell survival.
- term:
    id: GO:0090201
    label: negative regulation of release of cytochrome c from mitochondria
  evidence_type: IMP
  original_reference_id: PMID:16608849
  review:
    summary: FXN prevents cytochrome c release from mitochondria.
    action: KEEP_AS_NON_CORE
    reason: This anti-apoptotic effect is a secondary consequence of FXN function.
    supported_by:
    - reference_id: PMID:16608849
      supporting_text: 2006 Apr 11. A pool of extramitochondrial frataxin that promotes
        cell survival.
- term:
    id: GO:0034986
    label: iron chaperone activity
  evidence_type: IDA
  original_reference_id: PMID:15123683
  review:
    summary: Direct demonstration of iron chaperone activity - FXN delivers iron to
      ferrochelatase.
    action: ACCEPT
    reason: Iron chaperone activity is a core molecular function of FXN, delivering
      iron to both ferrochelatase and the ISC assembly complex.
    supported_by:
    - reference_id: PMID:15123683
      supporting_text: Herein we demonstrate Hs holofrataxin to be a high affinity
        iron binding partner for Hs ferrochelatase that is capable of both delivering
        iron to ferrochelatase and mediating the terminal step in mitochondrial heme
        biosynthesis
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  review:
    summary: Inferred from yeast ortholog.
    action: ACCEPT
    reason: Correct localization based on conserved function.
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: NAS
  original_reference_id: PMID:17285345
  review:
    summary: Mitochondrial matrix localization from iron-binding study.
    action: ACCEPT
    reason: Correct localization.
    supported_by:
    - reference_id: PMID:17285345
      supporting_text: '2007 Feb 7. N-terminal iron-mediated self-cleavage of human
        frataxin: regulation of iron binding and complex formation with target proteins.'
- term:
    id: GO:0008198
    label: ferrous iron binding
  evidence_type: IDA
  original_reference_id: PMID:12785837
  review:
    summary: Initial characterization of iron binding to frataxin.
    action: ACCEPT
    reason: Core molecular function well demonstrated.
    supported_by:
    - reference_id: PMID:12785837
      supporting_text: In this paper we demonstrate human frataxin to bind from six
        to seven iron ions.
- term:
    id: GO:0008198
    label: ferrous iron binding
  evidence_type: IDA
  original_reference_id: PMID:17285345
  review:
    summary: Iron binding study with N-terminal self-cleavage characterization.
    action: ACCEPT
    reason: Core molecular function.
    supported_by:
    - reference_id: PMID:17285345
      supporting_text: '2007 Feb 7. N-terminal iron-mediated self-cleavage of human
        frataxin: regulation of iron binding and complex formation with target proteins.'
- term:
    id: GO:0008199
    label: ferric iron binding
  evidence_type: IDA
  original_reference_id: PMID:12785837
  review:
    summary: Early study reporting ferric iron binding. Later NMR studies (PMID:29576242)
      show FXN preferentially binds Fe2+ not Fe3+.
    action: MARK_AS_OVER_ANNOTATED
    reason: More recent NMR evidence demonstrates FXN binds Fe2+ but not Fe3+ (PMID:29576242).
      The earlier reports of Fe3+ binding may reflect oxidation of bound Fe2+.
    supported_by:
    - reference_id: PMID:12785837
      supporting_text: Iron-sulfur cluster biosynthesis.
- term:
    id: GO:0016540
    label: protein autoprocessing
  evidence_type: IDA
  original_reference_id: PMID:12785837
  review:
    summary: FXN precursor undergoes two-step proteolytic processing by MPP to yield
      mature form. This is not autoprocessing but processing by mitochondrial processing
      peptidase.
    action: REMOVE
    reason: FXN is processed by mitochondrial processing peptidase (MPP), not by autoprocessing.
      The term is incorrect for FXN maturation.
    supported_by:
    - reference_id: PMID:12785837
      supporting_text: Iron-sulfur cluster biosynthesis.
- term:
    id: GO:0051537
    label: 2 iron, 2 sulfur cluster binding
  evidence_type: IDA
  original_reference_id: PMID:12785837
  review:
    summary: Some evidence for [2Fe-2S] binding was reported, but FXN's primary role
      is to facilitate cluster assembly on ISCU rather than to bind clusters itself.
    action: UNDECIDED
    reason: The evidence for [2Fe-2S] cluster binding by FXN is limited. More recent
      studies emphasize FXN's role in delivering iron and activating sulfur transfer
      rather than binding assembled clusters.
    supported_by:
    - reference_id: PMID:12785837
      supporting_text: Iron-sulfur cluster biosynthesis.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15123683
  review:
    summary: Interaction with ferrochelatase (FECH/P22830) demonstrated.
    action: ACCEPT
    reason: Functionally relevant interaction with ferrochelatase for iron delivery
      in heme biosynthesis.
    supported_by:
    - reference_id: PMID:15123683
      supporting_text: Herein we demonstrate Hs holofrataxin to be a high affinity
        iron binding partner for Hs ferrochelatase that is capable of both delivering
        iron to ferrochelatase and mediating the terminal step in mitochondrial heme
        biosynthesis
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: PMID:17468497
  review:
    summary: Experimental evidence for mitochondrial localization in vivo.
    action: ACCEPT
    reason: Well-established mitochondrial localization.
    supported_by:
    - reference_id: PMID:17468497
      supporting_text: Apr 27. In vivo maturation of human frataxin.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IDA
  original_reference_id: PMID:17468497
  review:
    summary: Evidence for cytosolic localization of some FXN forms.
    action: ACCEPT
    reason: Extramitochondrial frataxin exists in the cytosol.
    supported_by:
    - reference_id: PMID:17468497
      supporting_text: Apr 27. In vivo maturation of human frataxin.
- term:
    id: GO:0006879
    label: intracellular iron ion homeostasis
  evidence_type: IMP
  original_reference_id: PMID:18160053
  review:
    summary: FXN silencing disrupts iron homeostasis, rescued by mitochondrial ferritin
      expression.
    action: KEEP_AS_NON_CORE
    reason: Effect on iron homeostasis is indirect through disrupted Fe-S cluster
      assembly.
    supported_by:
    - reference_id: PMID:18160053
      supporting_text: The effects of frataxin silencing in HeLa cells are rescued
        by the expression of human mitochondrial ferritin.
- term:
    id: GO:0008198
    label: ferrous iron binding
  evidence_type: IDA
  original_reference_id: PMID:15123683
  review:
    summary: Fe2+ binding demonstrated in context of ferrochelatase delivery.
    action: ACCEPT
    reason: Core molecular function.
    supported_by:
    - reference_id: PMID:15123683
      supporting_text: 2004 Apr 27. Frataxin-mediated iron delivery to ferrochelatase
        in the final step of heme biosynthesis.
- term:
    id: GO:0008199
    label: ferric iron binding
  evidence_type: IDA
  original_reference_id: PMID:18537827
  review:
    summary: Study of FRDA clinical mutants and iron binding.
    action: MARK_AS_OVER_ANNOTATED
    reason: More recent NMR evidence (PMID:29576242) shows FXN binds Fe2+ but not
      Fe3+.
    supported_by:
    - reference_id: PMID:18537827
      supporting_text: Dynamics, stability and iron-binding activity of frataxin clinical
        mutants.
- term:
    id: GO:0010039
    label: response to iron ion
  evidence_type: IMP
  original_reference_id: PMID:18424449
  review:
    summary: FXN expression is regulated by iron levels.
    action: KEEP_AS_NON_CORE
    reason: FXN is regulated by iron, but this describes regulation of FXN rather
      than its function.
    supported_by:
    - reference_id: PMID:18424449
      supporting_text: 'Apr 17. Iron-dependent regulation of frataxin expression:
        implications for treatment of Friedreich ataxia.'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:15961414
  review:
    summary: Interaction with succinate dehydrogenase subunits SDHA (P31040) and SDHB
      (P21912) demonstrated.
    action: ACCEPT
    reason: Functionally relevant interactions with respiratory chain proteins containing
      Fe-S clusters.
    supported_by:
    - reference_id: PMID:15961414
      supporting_text: Frataxin interacts functionally with mitochondrial electron
        transport chain proteins.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to
    orthologs using Ensembl Compara
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
- id: PMID:12785837
  title: Iron-sulfur cluster biosynthesis. Characterization of frataxin as an iron
    donor for assembly of [2Fe-2S] clusters in ISU-type proteins.
  findings:
  - statement: FXN binds 6-7 iron ions with K_D(Fe2+) approximately 55 microM
  - statement: Holo frataxin forms complex with ISU with sub-micromolar affinity
  - statement: Iron-bound frataxin mediates iron transfer to ISU for [2Fe-2S] cluster
      assembly
- id: PMID:15123683
  title: Frataxin-mediated iron delivery to ferrochelatase in the final step of heme
    biosynthesis.
  findings:
  - statement: FXN is high affinity iron binding partner for ferrochelatase
  - statement: FXN delivers iron to ferrochelatase for heme biosynthesis
- id: PMID:15509595
  title: Iron-sulfur protein maturation in human cells - evidence for a function of
    frataxin.
  findings:
  - statement: FXN required for Fe-S protein maturation in human cells
- id: PMID:15641778
  title: Assembly of human frataxin is a mechanism for detoxifying redox-active iron.
  findings:
  - statement: Oligomeric FXN has ferroxidase activity (EC 1.16.3.1)
  - statement: Assembled FXN detoxifies redox-active iron
  - statement: Monomeric FXN lacks ferroxidase activity
- id: PMID:15961414
  title: Frataxin interacts functionally with mitochondrial electron transport chain
    proteins.
  findings:
  - statement: FXN interacts with SDHA and SDHB
- id: PMID:16608849
  title: A pool of extramitochondrial frataxin that promotes cell survival.
  findings:
  - statement: Extramitochondrial frataxin exists and promotes cell survival
- id: PMID:17285345
  title: N-terminal iron-mediated self-cleavage of human frataxin - regulation of
    iron binding and complex formation with target proteins.
  findings:
  - statement: Iron binding regulates FXN structure and interactions
- id: PMID:17468497
  title: In vivo maturation of human frataxin.
  findings:
  - statement: FXN processed in two steps to mature form (residues 81-210)
- id: PMID:18160053
  title: The effects of frataxin silencing in HeLa cells are rescued by the expression
    of human mitochondrial ferritin.
  findings:
  - statement: FXN silencing causes iron homeostasis defects
- id: PMID:18424449
  title: Iron-dependent regulation of frataxin expression - implications for treatment
    of Friedreich ataxia.
  findings:
  - statement: FXN expression regulated by iron levels
- id: PMID:18537827
  title: Dynamics, stability and iron-binding activity of frataxin clinical mutants.
  findings:
  - statement: Characterization of FRDA mutant iron binding
- id: PMID:20053667
  title: Molecular control of the cytosolic aconitase/IRP1 switch by extramitochondrial
    frataxin.
  findings:
  - statement: Extramitochondrial FXN modulates ACO1/IRP1 activity
- id: PMID:21298097
  title: Mammalian frataxin - an essential function for cellular viability through
    an interaction with a preformed ISCU/NFS1/ISD11 iron-sulfur assembly complex.
  findings:
  - statement: FXN interacts with preformed ISCU/NFS1/ISD11 complex
  - statement: Mature FXN(81-210) is the essential functional form
  - statement: Main interactors are NFS1, ISCU, ISD11
- id: PMID:24971490
  title: Human frataxin activates Fe-S cluster biosynthesis by facilitating sulfur
    transfer chemistry.
  findings:
  - statement: FXN accelerates sulfur transfer from NFS1 to ISCU
  - statement: FXN functions as allosteric activator, not just iron donor
  - statement: Persulfide on ISCU is viable for Fe-S cluster synthesis
- id: PMID:26702583
  title: Mitochondrial Hspa9/Mortalin regulates erythroid differentiation via iron-sulfur
    cluster assembly.
  findings:
  - statement: FXN interacts with HSPA9
- id: PMID:27519411
  title: Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery.
  findings:
  - statement: Structural characterization of human ISC complex
- id: PMID:28634302
  title: Structure of human Fe-S assembly subcomplex reveals unexpected cysteine desulfurase
    architecture and acyl-ACP-ISD11 interactions.
  findings:
  - statement: Structure of NFS1-ISD11-ACP subcomplex
- id: PMID:29097656
  title: Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis
    complex.
  findings:
  - statement: Structural dynamics of ISC complex
- id: PMID:29491838
  title: Iron Sulfur and Molybdenum Cofactor Enzymes Regulate the Drosophila Life
    Cycle by Controlling Cell Metabolism.
  findings:
  - statement: Drosophila study on Fe-S cluster enzymes cited for human FXN annotation
      by FlyBase
- id: PMID:29576242
  title: Interactions of iron-bound frataxin with ISCU and ferredoxin on the cysteine
    desulfurase complex leading to Fe-S cluster assembly.
  findings:
  - statement: FXN binds Fe2+ but not Fe3+
  - statement: FXN does not bind ISCU directly, only when both bound to (NIA)2 complex
  - statement: Iron released from FXN requires both L-cysteine and reductant
  - statement: Fe2+-FXN can serve as sole iron donor for cluster assembly in vitro
- id: PMID:31101807
  title: Structure of the human frataxin-bound iron-sulfur cluster assembly complex
    provides insight into its activation mechanism.
  findings:
  - statement: Cryo-EM structure of human FXN-bound ISC complex at 3.2 A
  - statement: FXN binds to preformed NIAU complex
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
- id: PMID:32814053
  title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins
    and Uncovers Widespread Protein Aggregation in Affected Brains.
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics
    in cellular context.
- id: PMID:38627381
  title: Mechanism and structural dynamics of sulfur transfer during de novo [2Fe-2S]
    cluster assembly on ISCU2.
  findings:
  - statement: High-resolution cryo-EM of sulfur transfer mechanism
  - statement: FXN optimally positions residues for rapid persulfide transfer
- id: Reactome:R-HSA-1362408
  title: FXN:NFS1:ISD11:ISCU assembles 2Fe-2S iron-sulfur cluster
- id: Reactome:R-HSA-1362409
  title: Mitochondrial iron-sulfur cluster biogenesis
- id: Reactome:R-HSA-1362416
  title: Frataxin binds iron
- id: Reactome:R-HSA-9854405
  title: Frataxin transfers Fe2+ to ACO2
- id: Reactome:R-HSA-9854984
  title: Transfer of Fe-S clusters to SDHB
- id: Reactome:R-HSA-9865881
  title: Complex III assembly
- id: Reactome:R-HSA-9866272
  title: 2Fe-2S is inserted in UQCRFS1
- id: file:human/FXN/FXN-deep-research-falcon.md
  title: Deep research report on FXN
  findings: []
core_functions:
- molecular_function:
    id: GO:0034986
    label: iron chaperone activity
  description: FXN binds Fe2+ and delivers it to the ISC assembly complex for [2Fe-2S]
    cluster synthesis. Iron is released from FXN only when the cysteine desulfurase
    is activated by L-cysteine and reductant, demonstrating regulated iron delivery.
    FXN also delivers iron to ferrochelatase for the terminal step of heme biosynthesis.
  locations:
  - id: GO:0005759
    label: mitochondrial matrix
  in_complex:
    id: GO:0099128
    label: mitochondrial [2Fe-2S] assembly complex
  supported_by:
  - reference_id: PMID:12785837
    supporting_text: Iron binding to frataxin has been quantitated by iron-dependent
      fluorescence measurements
  - reference_id: PMID:29576242
    supporting_text: Fe2+-FXN can serve as the sole iron donor for this process in
      vitro.
- molecular_function:
    id: GO:0008047
    label: enzyme activator activity
  description: FXN functions as an allosteric activator of the cysteine desulfurase
    NFS1, accelerating persulfide formation and sulfur transfer to ISCU. Recent cryo-EM
    structures show FXN optimally positions ISCU assembly-site residues to enable
    rapid sulfur transfer.
  directly_involved_in:
  - id: GO:0044571
    label: '[2Fe-2S] cluster assembly'
  locations:
  - id: GO:0005759
    label: mitochondrial matrix
  supported_by:
  - reference_id: PMID:24971490
    supporting_text: Previous in vitro results revealed a role for human FXN in activating
      the cysteine desulfurase and Fe-S cluster biosynthesis activities of the Fe-S
      assembly complex.
  - reference_id: PMID:38627381
    supporting_text: High-resolution cryo-EM structures obtained from anaerobically
      prepared samples provide snapshots that both visualize different stages of persulfide
      transfer from Cys381NFS1 to Cys138ISCU2 and clarify the molecular role of frataxin
      in optimally positioning assembly site residues for fast sulfur transfer
- molecular_function:
    id: GO:0008198
    label: ferrous iron binding
  description: FXN binds ferrous iron (Fe2+) with high affinity but does not bind
    ferric iron (Fe3+). The iron-binding site is located on the alpha1-beta1 face
    of the protein. Iron binding is essential for FXN's iron chaperone function.
  locations:
  - id: GO:0005759
    label: mitochondrial matrix
  supported_by:
  - reference_id: PMID:29576242
    supporting_text: FXN tightly binds a single Fe2+ but not Fe3+.
  - reference_id: PMID:12785837
    supporting_text: Iron binding to frataxin has been quantitated by iron-dependent
      fluorescence measurements [K(D)(Fe(3+)) approximately 11.7 microM; (K(D)(Fe(2+))
      approximately 55.0 microM] and isothermal titration calorimetry (ITC) [K(D)(Fe(3+))
      approximately 10.2 microM]
suggested_experiments:
- description: Quantitative analysis of FXN's relative contribution to [2Fe-2S] cluster
    assembly versus heme biosynthesis under different physiological conditions.
  hypothesis: FXN primarily functions in Fe-S cluster assembly with heme biosynthesis
    as a secondary role.
- description: Further characterization of the extramitochondrial frataxin pool and
    its functional significance.
  hypothesis: Extramitochondrial frataxin may have distinct regulatory functions independent
    of Fe-S cluster assembly.
suggested_questions:
- question: What is the in vivo iron source for frataxin, and how is iron delivered
    to FXN in the mitochondrial matrix?
- question: What is the physiological significance of the ferroxidase activity of
    oligomeric frataxin?
tags:
- iron-sulfur-cluster-biogenesis

FXN

Gene Description

Existing Annotations Review

Core Functions

FXN functions as an allosteric activator of the cysteine desulfurase NFS1, accelerating persulfide formation and sulfur transfer to ISCU. Recent cryo-EM structures show FXN optimally positions ISCU assembly-site residues to enable rapid sulfur transfer.

FXN binds ferrous iron (Fe2+) with high affinity but does not bind ferric iron (Fe3+). The iron-binding site is located on the alpha1-beta1 face of the protein. Iron binding is essential for FXN's iron chaperone function.

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