UniProt: Q969G6 (RIFK_HUMAN), 155 aa, EC 2.7.1.26. HGNC:30324, chromosome 9. Gene ID 55312.
RFK is riboflavin kinase (flavokinase, ATP:riboflavin 5'-phosphotransferase),
the first committed and rate-limiting step of flavin-cofactor biosynthesis in
humans. It phosphorylates riboflavin (vitamin B2) using ATP to produce flavin
mononucleotide (FMN); FMN is subsequently adenylylated to FAD by FAD synthase
(FLAD1). The reaction requires a divalent metal (Zn2+ or Mg2+).
riboflavin + ATP = FMN + ADP + H(+), EC 2.7.1.26Crystal structures of human RFK: six-stranded antiparallel beta barrel core,
similar to the riboflavin synthase / ferredoxin-reductase FAD-binding fold; an
intrinsically bound MgADP defines a novel nucleotide-binding motif; catalysis
proposed through the active-site "arch"
PMID:12623014.
PDB: 1NB0, 1NB9, 1P4M, 1Q9S. ACT_SITE Glu79 (nucleophile). Mutagenesis E79Q
abolishes riboflavin kinase activity but not TNFRSF1A/CYBA binding
[file:human/RFK/RFK-uniprot.txt "E->Q: Loss of riboflavin kinase activity."].
PMID:12623014 is a structure paper; GOA also uses it as the NAS source for the
function/localization/pathway statements (author narrative), which is reasonable
but lower-value than the IDA/experimental support.
Yazdanpanah et al. (Nature 2009) identified RFK as a TNFR1 (TNFRSF1A)-binding
protein that physically and functionally couples TNFR1 to NADPH oxidase. RFK
binds the TNFR1 death domain and the NADPH oxidase subunit p22phox (CYBA);
bridging is required for TNF-induced (not TLR-induced) ROS production. RFK's
enzymatic role — providing FAD, an essential prosthetic group of NADPH oxidase —
underlies the ROS phenotype (exogenous FMN/FAD substitutes for TNF stimulation in
RFK-deficient cells).
PMID:19641494
PMID:19641494
This is the source of the experimental annotations to apoptotic process
(GO:0006915, IMP), positive regulation of NAD(P)H oxidase activity (GO:0033864,
IMP), and protein binding (GO:0005515, IPI vs TNFRSF1A/P19438). These describe a
context-specific signaling role that is downstream of / built on the core flavokinase
activity — treated as KEEP_AS_NON_CORE (regulatory processes) or
MARK_AS_OVER_ANNOTATED (bare protein binding), not core evolved functions.
UniProt SUBCELLULAR LOCATION: Cytoplasm (ECO:0000250)
[file:human/RFK/RFK-uniprot.txt "SUBCELLULAR LOCATION: Cytoplasm"]. Reactome
describes RFK as "a cytosolic enzyme." So cytoplasm / cytosol is the core location.
Other localization annotations are lower-confidence high-throughput / IEA calls:
- GO:0005739 mitochondrion — IBA (GO_REF:0000033) and HTP (PMID:34800366, a
large-scale mitochondrial-proteome dataset). Not the primary site; a flavokinase
supplies flavin cofactors cytosolically, and MitoCarta-type datasets frequently
include cytosolic contaminants. Kept as non-core (do not remove HTP experimental-
type; the IBA can be marked over-annotated).
- GO:0005794 Golgi apparatus — IDA from HPA immunofluorescence (GO_REF:0000052).
Single antibody-based localization; not corroborated by UniProt or biochemistry.
Marked as over-annotated (do not REMOVE — IDA experimental type).
All bare protein binding (GO:0005515) IPI annotations → MARK_AS_OVER_ANNOTATED
(never REMOVE per policy; uninformative MF for the pathway/core-function view).
Core (ACCEPT): riboflavin kinase activity (IDA, IBA, TAS, and the two IEA/NAS
duplicates for MF); FMN biosynthetic process; riboflavin metabolic process;
cytosol. FAD/FMN biosynthesis is the evolved function.
riboflavin biosynthetic process (GO:0009231, IEA InterPro2GO & NAS) is
technically a mislabel for a human context — humans do not synthesize the
riboflavin ring de novo; RFK acts in riboflavin utilization (FMN/FAD synthesis),
i.e. riboflavin metabolic process. MODIFY → GO:0006771 riboflavin metabolic
process (the IEA one); the NAS one likewise MODIFY.
Non-core / signaling: apoptotic process, positive regulation of NAD(P)H oxidase
activity (both IMP, KEEP_AS_NON_CORE — real moonlighting downstream of catalytic
function).