RFK

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0008531 riboflavin kinase activity	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) inference of riboflavin kinase activity, the core, well-conserved molecular function of this family. Directly confirmed for human RFK by experimental assay (IDA, PMID:19641494) and by the crystal structures and catalytic-activity annotation in UniProt. Accept as a core function. Supporting Evidence: file:human/RFK/RFK-uniprot.txt EC=2.7.1.26
GO:0006771 riboflavin metabolic process	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic inference that RFK participates in riboflavin (vitamin B2) metabolism. This is accurate: RFK converts riboflavin to FMN, the entry point of flavin-cofactor utilization. Accept as a core biological process. Supporting Evidence: file:human/RFK/RFK-uniprot.txt FUNCTION: Catalyzes the phosphorylation of riboflavin (vitamin B2) to
GO:0005739 mitochondrion	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Phylogenetic (IBA) inference of mitochondrial localization, propagated in part from the yeast ortholog. Human RFK is annotated by UniProt and Reactome as a cytoplasmic/ cytosolic enzyme, and a flavokinase supplies flavin cofactors from the cytosol. The mitochondrion is not the primary site of action for the human protein; keep as a non-core localization. Reason: Examined as a synthesis row. The PAINT IBD for GO:0005739 at PTN000507879 (PTHR22749-paint.tsv) has a single seed, yeast FMN1 (SGD:S000002644), whose experimental location is the mitochondrial inner membrane and microsomes (PMID:10887197); the node carries only the organelle. For human RFK the organelle claim is independently supported by the MitoCoP high-confidence proteome HTP row (PMID:34800366), so it is kept, non-core, matching that row; the curated human location is cytoplasm and the core activity is assigned to the cytosol. The yeast inner-membrane detail does not transfer: yeast Fmn1 has an N-terminal hydrophobic segment (MFTWTIYVSLLLVLAGTFLM) and a predicted import signal, whereas human RFK (155 aa) has neither a transit peptide nor a TM segment in UniProt. With one ortholog-based line against the human sequence features, no sub-compartment is added. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000507879 · PTN000507879 SUPPORTS TRANSFER Node seeded only by yeast FMN1, whose inner-membrane (IDA, PMID:10887197) location is carried at the node as the root organelle. Correct at organelle level for human RFK given the MitoCoP HTP detection; the membrane-anchored inner-membrane form is not inferred for the human protein, which lacks the yeast N-terminal hydrophobic segment. SGD:S000002644 · FMN1 SUPPORTS SOURCE BUT NOT TARGET Sound source for yeast (submitochondrial fractionation). Its inner-membrane sub-compartment depends on a hydrophobic N-terminus absent from human RFK, so only the organelle-level claim is taken to apply to the human protein. Supporting Evidence: file:human/RFK/RFK-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm PMID:10887197 Analysis of submitochondrial fractions revealed that the mitochondrial form of Fmn1p is an integral protein of the inner membrane exposing its COOH-terminal domain to the matrix space.
GO:0009398 FMN biosynthetic process	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic inference that RFK is involved in FMN biosynthesis. This is the precise product-forming process for riboflavin kinase (riboflavin -> FMN) and matches the UniProt pathway annotation "FMN from riboflavin (ATP route): step 1/1". Accept as a core biological process. Supporting Evidence: file:human/RFK/RFK-uniprot.txt (ATP route): step 1/1.
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: Electronic mapping from the UniProt subcellular-location keyword. Consistent with the curated UniProt "Cytoplasm" location and with Reactome describing RFK as a cytosolic enzyme. Accept; the more specific cytosol term (GO:0005829) is the preferred core location. Supporting Evidence: file:human/RFK/RFK-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0008531 riboflavin kinase activity	IEA GO_REF:0000120	ACCEPT	Summary: Electronic assignment of riboflavin kinase activity from InterPro/RHEA/EC pipelines (EC 2.7.1.26, RHEA:14357). Fully concordant with the experimental IDA annotation and UniProt catalytic-activity statement. Accept (duplicate of the core molecular function). Supporting Evidence: file:human/RFK/RFK-uniprot.txt Reaction=riboflavin + ATP = FMN + ADP + H(+)
GO:0009231 riboflavin biosynthetic process	IEA GO_REF:0000002	MODIFY	Summary: InterPro2GO electronic mapping to riboflavin biosynthetic process. This is imprecise for the human enzyme: humans do not synthesize the riboflavin ring de novo (riboflavin is a dietary vitamin), and RFK acts in riboflavin utilization/salvage, converting riboflavin to FMN. The correct process is riboflavin metabolic process (or, more specifically, FMN biosynthetic process). Modify to riboflavin metabolic process. Proposed replacements: riboflavin metabolic process Supporting Evidence: file:human/RFK/RFK-uniprot.txt form flavin-mononucleotide (FMN), hence rate-limiting enzyme in the
GO:0009398 FMN biosynthetic process	IEA GO_REF:0000120	ACCEPT	Summary: Electronic assignment (InterPro/UniPathway UPA00276) of FMN biosynthetic process. Correct and precise for riboflavin kinase; duplicate of the IBA annotation to the same term. Accept. Supporting Evidence: file:human/RFK/RFK-uniprot.txt (ATP route): step 1/1.
GO:0005515 protein binding	IPI PMID:19641494 Riboflavin kinase couples TNF receptor 1 to NADPH oxidase.	MODIFY	Summary: IPI annotation from a curated physical interaction with TNFRSF1A (P19438) reported in Yazdanpanah et al. RFK binds the TNFR1 death domain and, via p22phox (CYBA), bridges TNFR1 to NADPH oxidase. The interaction is real and biologically meaningful, but the bare "protein binding" term is uninformative about RFK's molecular function. Reason: The cited paper identifies the partner and the binding site, so the row can carry a more informative binding term than bare protein binding: RFK binds the death domain of TNFR1 (TNFRSF1A). This is a non-core signalling role; the catalytic riboflavin kinase activity remains the core function. Proposed replacements: tumor necrosis factor receptor binding Supporting Evidence: PMID:19641494 previously unrecognized TNF-receptor-1 (TNFR1)-binding protein that physically PMID:19641494 RFK binds to both the TNFR1-death domain and to p22(phox)
GO:0005515 protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	REMOVE	Summary: IPI annotation from the HuRI human binary interactome (yeast two-hybrid), recording an interaction with CNTLN (Q9NXG0-2), also captured in UniProt. This is an uncharacterized high-throughput interaction with no established functional consequence, and the bare "protein binding" term is uninformative. Reason: Removed under the protein-binding policy because the row identifies no molecular function; the HuRI screen gives no more informative term to substitute. Removal does not mean the CNTLN interaction is false. Supporting Evidence: file:human/RFK/RFK-uniprot.txt Q969G6; Q9NXG0-2: CNTLN; NbExp=3;
GO:0006771 riboflavin metabolic process	TAS Reactome:R-HSA-196843	ACCEPT	Summary: Author/curator (TAS) annotation from the Reactome "Vitamin B2 (riboflavin) metabolism" pathway. Accurately places RFK in riboflavin metabolism. Accept as a core process. Supporting Evidence: Reactome:R-HSA-196964 This reaction is catalyzed by riboflavin kinase (RFK)
GO:0008531 riboflavin kinase activity	TAS Reactome:R-HSA-196964	ACCEPT	Summary: Author/curator (TAS) annotation from the Reactome reaction "RFK:Mg2+ phosphorylates RIB", describing RFK phosphorylating riboflavin to FMN using zinc or magnesium. Correct core molecular function. Accept. Supporting Evidence: Reactome:R-HSA-196964 It utilizes either zinc or magnesium ions in the reaction.
GO:0005794 Golgi apparatus	IDA GO_REF:0000052	MARK AS OVER ANNOTATED	Summary: IDA from Human Protein Atlas immunofluorescence. This single antibody-based localization is not corroborated by the curated UniProt subcellular location (cytoplasm) or by Reactome (cytosolic enzyme), and there is no biochemical rationale for Golgi localization of a soluble flavokinase. Treat as over-annotation rather than a core location (per policy, do not remove an experimental/IDA annotation). Supporting Evidence: file:human/RFK/RFK-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0005739 mitochondrion	HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an...	KEEP AS NON CORE	Summary: High-throughput proteomics detection in a quantitative human mitochondrial-proteome dataset. Large-scale organellar proteomes routinely include cytosolic proteins, and the curated UniProt/Reactome localization for RFK is cytoplasmic/cytosolic. Keep as a non-core localization; the mitochondrion is not the primary site of RFK action. Reason: Direct but assay-limited evidence: the MitoCoP quantitative proteome of purified human mitochondria resolves the organelle, not a sub-compartment, so the root term is what the experiment showed. Kept non-core because the curated location and the riboflavin-to-FMN step that feeds cytosolic FAD synthesis are cytoplasmic; human RFK has no transit peptide or TM segment, so there is no basis for a sub-compartment. Supporting Evidence: file:human/RFK/RFK-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0006771 riboflavin metabolic process	IDA PMID:19641494 Riboflavin kinase couples TNF receptor 1 to NADPH oxidase.	ACCEPT	Summary: Experimental (IDA) annotation to riboflavin metabolic process from Yazdanpanah et al., which demonstrated RFK's riboflavin kinase activity and its rate-limiting role in FAD synthesis. Correct core process. Accept. Supporting Evidence: PMID:19641494 rate-limiting in the synthesis of FAD, an essential prosthetic group of NADPH
GO:0008531 riboflavin kinase activity	IDA PMID:19641494 Riboflavin kinase couples TNF receptor 1 to NADPH oxidase.	ACCEPT	Summary: Direct experimental demonstration (IDA) of riboflavin kinase activity for human RFK (catalytic activity established, EC 2.7.1.26; E79Q active-site mutant abolishes the activity). This is the primary evidence for the core molecular function. Accept. Supporting Evidence: file:human/RFK/RFK-uniprot.txt E->Q: Loss of riboflavin kinase activity. No effect
GO:0006915 apoptotic process	IMP PMID:19641494 Riboflavin kinase couples TNF receptor 1 to NADPH oxidase.	KEEP AS NON CORE	Summary: IMP annotation reflecting RFK's role in TNFR1 signaling: by coupling TNFR1 to NADPH oxidase and enabling TNF-induced ROS production, RFK acts upstream of/within TNF-driven cell-death responses. This is a context-specific signaling/moonlighting role downstream of the catalytic function, not the core evolved function of the enzyme. Keep as a non-core process. Supporting Evidence: PMID:19641494 prerequisite for TNF-induced but not for Toll-like-receptor-induced ROS
GO:0033864 positive regulation of NAD(P)H oxidase activity	IMP PMID:19641494 Riboflavin kinase couples TNF receptor 1 to NADPH oxidase.	KEEP AS NON CORE	Summary: IMP annotation: RFK physically and functionally couples TNFR1 to NADPH oxidase and, by supplying FAD (an essential prosthetic group of the oxidase), positively regulates TNF-induced NADPH oxidase activity/ROS production. Well supported experimentally but a specialized signaling role rather than the core flavokinase function. Keep as a non-core process. Supporting Evidence: PMID:19641494 binds to both the TNFR1-death domain and to p22(phox), the common subunit of
GO:0005829 cytosol	TAS Reactome:R-HSA-196964	ACCEPT	Summary: Author/curator (TAS) annotation from Reactome placing RFK in the cytosol; Reactome explicitly describes it as "a cytosolic enzyme". This is the preferred, specific core location, concordant with the UniProt cytoplasm call. Accept. Supporting Evidence: Reactome:R-HSA-196964 a cytosolic enzyme existing as a monomer
GO:0005737 cytoplasm	NAS PMID:12623014 Crystal structure of human riboflavin kinase reveals a beta ...	ACCEPT	Summary: Author-statement (NAS) cytoplasmic localization from the human RFK structure paper. Consistent with the curated UniProt location and Reactome. The more specific cytosol term is preferred, but this is correct. Accept. Supporting Evidence: file:human/RFK/RFK-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0008531 riboflavin kinase activity	NAS PMID:12623014 Crystal structure of human riboflavin kinase reveals a beta ...	ACCEPT	Summary: Author-statement (NAS) of riboflavin kinase activity from the human RFK crystal-structure paper, which describes RFK as "an essential enzyme catalyzing the phosphorylation of riboflavin (vitamin B(2)) to form FMN". Correct core molecular function; corroborated by the IDA experimental annotation. Accept. Supporting Evidence: PMID:12623014 an essential enzyme catalyzing the phosphorylation of
GO:0009231 riboflavin biosynthetic process	NAS PMID:12623014 Crystal structure of human riboflavin kinase reveals a beta ...	MODIFY	Summary: Author-statement (NAS) to riboflavin biosynthetic process. As with the InterPro2GO IEA call, this is imprecise for the human enzyme: humans acquire riboflavin from the diet and do not synthesize the ring de novo; RFK carries out riboflavin utilization (FMN/FAD synthesis). The paper frames RFK's step as "vitamin B(2) utilization and flavin cofactor synthesis". Modify to riboflavin metabolic process. Proposed replacements: riboflavin metabolic process Supporting Evidence: PMID:12623014 obligatory step in vitamin B(2)

Gene Description

Existing Annotations Review

Core Functions

Riboflavin kinase activity: phosphorylation of riboflavin (vitamin B2) by ATP to form FMN, releasing ADP, using a divalent metal ion (Zn2+ or Mg2+). This is the first, rate-limiting step of FMN/FAD cofactor biosynthesis.

References

📚 Additional Documentation

Notes

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