FMN1 (YDR236C) encodes the monofunctional riboflavin kinase (flavokinase, EC 2.7.1.26) of S. cerevisiae, which phosphorylates riboflavin with ATP to form FMN, the first step in conversion of riboflavin to flavin cofactors. Unlike bacterial bifunctional RibF enzymes, Fmn1 has no FAD synthetase activity; FAD is made from FMN by the unrelated Fad1. Deletion of FMN1 prevents growth on rich medium unless FMN is supplied. Fmn1 is a 25-kDa membrane-associated protein found mostly (~90%) in microsomal (ER) fractions and ~10% in mitochondria, where it is an integral inner-membrane protein with its C-terminal catalytic domain facing the matrix, providing intramitochondrial FMN.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: Mitochondrial activity inherited from a fungal sub-node with yeast Fmn1 as source; consistent with fractionation showing ~10% of Fmn1 in mitochondria. Supporting Evidence: PMID:10887197 we provide evidence that the Fmn1 protein is localized in microsomes and in mitochondria file:yeast/FMN1/FMN1-uniprot.txt Note=90% microsomal. 10% mitochondrial. |
| GO:0005743 mitochondrial inner membrane | IDA PMID:10887197 Molecular characterization of FMN1, the structural gene for ... | ACCEPT | Summary: Submitochondrial fractionation showed the mitochondrial form of Fmn1 is an integral inner-membrane protein with its C-terminal domain in the matrix. Supporting Evidence: 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:0005743 mitochondrial inner membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt mapping of 'Mitochondrion inner membrane' from Santos et al. 2000 submitochondrial fractionation; correct. Supporting Evidence: 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:0005783 endoplasmic reticulum | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt mapping of 'Endoplasmic reticulum', inferred (ECO:0000305) from the microsomal fraction in which ~90% of Fmn1 is found. Microsomes are largely ER-derived, so this is a reasonable reading; direct ER imaging is lacking. Supporting Evidence: PMID:10887197 we provide evidence that the Fmn1 protein is localized in microsomes and in mitochondria file:yeast/FMN1/FMN1-uniprot.txt Note=90% microsomal. 10% mitochondrial. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | MARK AS OVER ANNOTATED | Summary: Pathway-default cytosol from YeastPathways. Experimental fractionation places Fmn1 in microsomal and mitochondrial-inner-membrane fractions rather than the soluble cytosol; the catalytic domain of the microsomal form may face the cytosol, but this has not been shown. Reason: Membrane-associated protein; soluble cytosolic location is not supported by fractionation data. Supporting Evidence: PMID:10887197 we provide evidence that the Fmn1 protein is localized in microsomes and in mitochondria file:yeast/FMN1/FMN1-uniprot.txt Note=90% microsomal. 10% mitochondrial. |
| GO:0006771 riboflavin metabolic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Riboflavin metabolic process: Fmn1 consumes riboflavin, so this is correct but more general than the FMN biosynthetic process it actually performs. Reason: Accurate parent-level process; FMN biosynthetic process is the specific core BP. Supporting Evidence: PMID:10887197 The purified form of the expressed recombinant protein efficiently catalyzed the formation of FMN from riboflavin and ATP. |
| GO:0008531 riboflavin kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Riboflavin kinase activity inherited from the flavokinase family node (human RFK Q969G6, S. pombe Fmn1, plant and bacterial RibF), with yeast FMN1 as an experimental source. Core MF. Supporting Evidence: PMID:10887197 The purified form of the expressed recombinant protein efficiently catalyzed the formation of FMN from riboflavin and ATP. file:yeast/FMN1/FMN1-uniprot.txt Reaction=riboflavin + ATP = FMN + ADP + H(+); Xref=Rhea:RHEA:14357, |
| GO:0008531 riboflavin kinase activity | IDA PMID:10887197 Molecular characterization of FMN1, the structural gene for ... | ACCEPT | Summary: Purified recombinant Fmn1 catalysed FMN formation from riboflavin and ATP, without FAD synthetase activity. Core MF. Supporting Evidence: PMID:10887197 The purified form of the expressed recombinant protein efficiently catalyzed the formation of FMN from riboflavin and ATP. PMID:10887197 In contrast to bifunctional prokaryotic flavokinase/FAD synthetase enzymes, the yeast enzyme did not show accompanying FAD synthetase activity. |
| GO:0008531 riboflavin kinase activity | IDA PMID:12614612 Interaction and assembly of murine pre-replicative complex p... | ACCEPT | Summary: The cited paper (Kneissl et al. 2003) is a yeast two-hybrid study of murine pre-replicative complex proteins; its abstract contains nothing about flavokinase or yeast FMN1, so this PMID is very likely a mis-entered reference. The function itself is correct and independently established (PMID:10887197), but this specific evidence row cannot be verified. Reason: The asserted activity is correct for FMN1 and is established independently by the purified recombinant enzyme (PMID:10887197), so the claim is accepted and the curator's row is not removed. The evidence link is doubtful, not the function. The row was assigned by MGI to a yeast protein and cites a murine pre-replicative-complex two-hybrid paper (full text not cached), so the reference is recorded as a suspected upstream defect for MGI to check. Supporting Evidence: PMID:10887197 The purified form of the expressed recombinant protein efficiently catalyzed the formation of FMN from riboflavin and ATP. |
| GO:0008531 riboflavin kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (InterPro riboflavin kinase IPR015865/IPR023465, RHEA:14357, EC 2.7.1.26); correct. Supporting Evidence: file:yeast/FMN1/FMN1-uniprot.txt Reaction=riboflavin + ATP = FMN + ADP + H(+); Xref=Rhea:RHEA:14357, |
| GO:0008531 riboflavin kinase activity | IMP PMID:10887197 Molecular characterization of FMN1, the structural gene for ... | ACCEPT | Summary: Overexpression raised flavokinase activity 50-fold and deletion caused FMN-rescuable growth defects, supporting Fmn1 as the cellular flavokinase. Supporting Evidence: PMID:10887197 Overexpression of YDR236c caused a 50-fold increase in flavokinase specific activity in yeast cells. PMID:10887197 Deletion of YDR236c produced yeast mutants unable to grow on rich medium; however, the growth of the ydr236cDelta mutants could be rescued by the addition of FMN to the medium. |
| GO:0008531 riboflavin kinase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways assigns riboflavin + ATP -> FMN (EC 2.7.1.26) to Fmn1; correct. Supporting Evidence: PMID:10887197 The purified form of the expressed recombinant protein efficiently catalyzed the formation of FMN from riboflavin and ATP. |
| GO:0009231 riboflavin biosynthetic process | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO from the riboflavin kinase domain superfamily (IPR023465) maps to riboflavin biosynthesis. This is wrong for Fmn1: riboflavin kinase consumes riboflavin to make FMN and plays no part in de novo riboflavin synthesis (Rib1-Rib7 pathway). The InterPro2GO mapping is an over-reach for this domain. Supporting Evidence: PMID:10887197 The purified form of the expressed recombinant protein efficiently catalyzed the formation of FMN from riboflavin and ATP. file:yeast/FMN1/FMN1-uniprot.txt Reaction=riboflavin + ATP = FMN + ADP + H(+); Xref=Rhea:RHEA:14357, |
| GO:0009398 FMN biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: FMN biosynthesis inherited from the flavokinase node; Fmn1 is the sole yeast riboflavin kinase. Core BP. Supporting Evidence: PMID:10887197 The purified form of the expressed recombinant protein efficiently catalyzed the formation of FMN from riboflavin and ATP. PMID:10887197 Deletion of YDR236c produced yeast mutants unable to grow on rich medium; however, the growth of the ydr236cDelta mutants could be rescued by the addition of FMN to the medium. |
| GO:0009398 FMN biosynthetic process | IDA PMID:10887197 Molecular characterization of FMN1, the structural gene for ... | ACCEPT | Summary: Direct production of FMN by purified Fmn1 places it in FMN biosynthesis. Supporting Evidence: PMID:10887197 The purified form of the expressed recombinant protein efficiently catalyzed the formation of FMN from riboflavin and ATP. |
| GO:0009398 FMN biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (InterPro IPR015865, UniPathway UPA00276 FMN from riboflavin); correct. Supporting Evidence: file:yeast/FMN1/FMN1-uniprot.txt Reaction=riboflavin + ATP = FMN + ADP + H(+); Xref=Rhea:RHEA:14357, |
| GO:0009398 FMN biosynthetic process | IMP PMID:10887197 Molecular characterization of FMN1, the structural gene for ... | ACCEPT | Summary: fmn1 deletion mutants require exogenous FMN, showing Fmn1 is needed for FMN synthesis in vivo. Supporting Evidence: PMID:10887197 Deletion of YDR236c produced yeast mutants unable to grow on rich medium; however, the growth of the ydr236cDelta mutants could be rescued by the addition of FMN to the medium. |
| GO:0042727 flavin-containing compound biosynthetic process | RCA GO_REF:0000123 | TOO GENERAL | Summary: Flavin-containing compound biosynthesis from the YeastPathways superpathway; FMN is a flavin, so correct but less specific than FMN biosynthetic process. Supporting Evidence: PMID:10887197 The purified form of the expressed recombinant protein efficiently catalyzed the formation of FMN from riboflavin and ATP. |
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Download this section (compressed HTML)Q: What membrane anchor gives Fmn1 integral-membrane behaviour in both microsomes and the mitochondrial inner membrane, and which side of the ER membrane does the catalytic domain face?
Q: Which publication was intended for the SGD IDA riboflavin kinase annotation currently attributed to PMID:12614612?
Riboflavin kinase, produces riboflavin monophosphate (FMN); FMN is a necessary cofactor for many enzymes; predominantly localizes to the microsomal fraction and also found in the mitochondrial inner membrane; human RFK functionally complements the lethality of the null mutation
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