RIB7 (YBR153W) encodes 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DAROPP) reductase (EC 1.1.1.302), the second enzyme of riboflavin (vitamin B2) biosynthesis in Saccharomyces cerevisiae. Following GTP cyclohydrolase II (Rib1), Rib7 reduces the ribosyl side chain of DAROPP to the ribityl chain using NAD(P)H, giving DARIPP, which is then deaminated by Rib2. This order (reduction before deamination) is characteristic of fungi and archaea and is the reverse of the bacterial/plant RibD/RibG route, whose reductase domain acts on the deaminated uracil (AROPP). Rib7 is a soluble homodimer of the dihydrofolate-reductase-like RibD C-terminal (HTP reductase) fold; the crystal structure with NADPH shows a conserved glycine-rich NADPH pyrophosphate-binding motif, and Thr35 (a lysine in bacterial RibD) governs preference for the 2-amino pyrimidinone substrate. rib7 mutants are riboflavin auxotrophs that accumulate a triaminopyrimidine derivative.
Definition: Catalysis of the reaction: 2,5-diamino-6-(1-D-ribitylamino)pyrimidin-4(3H)-one 5'-phosphate + NAD(P)+ = 2,5-diamino-6-(1-D-ribosylamino)pyrimidin-4(3H)-one 5'-phosphate + NAD(P)H + H+.
Justification: EC 1.1.1.302 (RHEA:27274, RHEA:27278) is the fungal/archaeal riboflavin pathway reductase (yeast Rib7) acting before deamination. GO currently only has GO:0008703 (EC 1.1.1.193), which names the deaminated uracil substrate of bacterial RibD, so fungal and archaeal reductases are annotated with a term for a different reaction.
Parent term: oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways (YEAST-RIBOSYN-PWY) places the Rib7 step in the cytosol. Rib7 is a soluble 244-residue protein with no recognisable targeting sequence and no direct localisation study contradicts a cytosolic site; the assignment is a pathway-level inference but reasonable. Supporting Evidence: PMID:23620735 Saccharomyces cerevisiae RIB7 (ScRIB7) is a potent target for anti-fungal agents because of its involvement in the riboflavin biosynthesis pathway as a NADPH-dependent reductase. |
| GO:0008703 5-amino-6-(5-phosphoribosylamino)uracil reductase activity | IDA PMID:23620735 Structural and functional insights into Saccharomyces cerevi... | ACCEPT | Summary: Lv et al. 2013 purified recombinant Rib7, solved its structure with NADPH and assayed NADPH-dependent reduction of both DAROPP (physiological fungal substrate) and AROPP (the bacterial RibD substrate named in GO:0008703). Wild-type Rib7 reduces AROPP in vitro but prefers DAROPP. GO has no term for the DAROPP reductase reaction (EC 1.1.1.302), so GO:0008703 is the closest available term; it is accepted with the caveat that the in vivo substrate differs at C2 (see proposed_new_terms). Supporting Evidence: PMID:23620735 ScRIB7 catalyzes reduction of DAROPP, while bacterial RibD catalyzes reduction of AROPP. PMID:23620735 Results showed that AROPP was recognized much better (by about 3 fold) by the T35K mutant than DAROPP, while the wild type was better at recognizing DAROPP PMID:23620735 Saccharomyces cerevisiae RIB7 (ScRIB7) is a potent target for anti-fungal agents because of its involvement in the riboflavin biosynthesis pathway as a NADPH-dependent reductase. |
| GO:0008703 5-amino-6-(5-phosphoribosylamino)uracil reductase activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro RibD C-terminal/HTP-reductase domain mapping (IPR002734, IPR011549) to GO:0008703. Correct domain, and the mapped term is the closest GO term for the fungal DAROPP reductase activity, though strictly it names the bacterial AROPP substrate. Supporting Evidence: PMID:23620735 In archaea and fungi, DAROPP is reduced at the phosphoribosyl moiety by RIB7 yielding 2, 5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5′-phosphate (DARIPP), which is then deaminated into 5-amino-6-ribitylamino-2,4 (1H,3H)-pyrimidinedione 5′-phosphate (ARIPP) by RIB2 |
| GO:0008703 5-amino-6-(5-phosphoribosylamino)uracil reductase activity | IMP PMID:4555411 Biosynthesis of riboflavine in Saccharomyces cerevisiae: the... | ACCEPT | Summary: Oltmanns & Bacher 1972 double-mutant epistasis and accumulation analysis assigned rib7 to the second enzyme of the pathway (the reductase step). The curator IMP is consistent with the later biochemistry; the cached record is abstract-only, so the specific assay cannot be checked. Supporting Evidence: PMID:4555411 The results support the conclusion that the genes rib(1) and rib(7) code for the first and second enzyme of the riboflavine pathway, respectively. |
| GO:0008703 5-amino-6-(5-phosphoribosylamino)uracil reductase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways RCA assigning Rib7 to the DAROPP -> DARIPP reduction of the riboflavin pathway. The reaction assignment is correct; the GO term used is the nearest available (AROPP reductase). Supporting Evidence: PMID:23620735 In archaea and fungi, DAROPP is reduced at the phosphoribosyl moiety by RIB7 yielding 2, 5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5′-phosphate (DARIPP), which is then deaminated into 5-amino-6-ribitylamino-2,4 (1H,3H)-pyrimidinedione 5′-phosphate (ARIPP) by RIB2 |
| GO:0009231 riboflavin biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (ARBA, InterPro, UniPathway UPA00275) for riboflavin biosynthesis. Correct for Rib7. Supporting Evidence: file:yeast/RIB7/RIB7-uniprot.txt -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis. |
| GO:0009231 riboflavin biosynthetic process | IMP PMID:5366000 Biochemical and genetic classification of riboflavine defici... | ACCEPT | Summary: Classical genetic/biochemical classification of riboflavin-deficient mutants (Oltmanns et al. 1969) identified rib7 among riboflavin auxotrophs. Abstract-only record; deferring to the SGD curator, and the role is fully consistent with later work. Supporting Evidence: PMID:4555411 The results support the conclusion that the genes rib(1) and rib(7) code for the first and second enzyme of the riboflavine pathway, respectively. |
| GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA GO_REF:0000117 | MODIFY | Summary: ARBA-predicted CH-OH/NAD(P) oxidoreductase activity. True for Rib7 (it oxidises/reduces the ribityl C1' alcohol with NAD(P)) but it is the direct parent of the more informative GO:0008703, which Rib7 already carries. Proposed replacements: 5-amino-6-(5-phosphoribosylamino)uracil reductase activity Supporting Evidence: PMID:23620735 Saccharomyces cerevisiae RIB7 (ScRIB7) is a potent target for anti-fungal agents because of its involvement in the riboflavin biosynthesis pathway as a NADPH-dependent reductase. |
| GO:0042727 flavin-containing compound biosynthetic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways superpathway 'riboflavin, FMN and FAD biosynthesis' yields the general flavin biosynthesis term. Rib7 acts only in the riboflavin branch (not in FMN/FAD formation by Fmn1/Fad1), so the more specific riboflavin biosynthetic process is the right term. Proposed replacements: riboflavin biosynthetic process Supporting Evidence: file:yeast/RIB7/RIB7-uniprot.txt -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis. |
| GO:0050661 NADP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro IPR011549 mapping to NADP binding. Supported directly by the Rib7-NADPH co-crystal structure; it is the cofactor-binding aspect of the reductase activity rather than an independent function. Supporting Evidence: PMID:23620735 A conserved G(76)-X-G(78)-Xn-G(181)-G(182) motif is present at the NADPH pyrophosphate group binding site. |
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Download this section (compressed HTML)Q: Should GO add a distinct term for EC 1.1.1.302 (DAROPP reductase) so that fungal Rib7 and archaeal orthologs are not annotated to the bacterial AROPP reductase term GO:0008703?
Experiment: Determine steady-state kinetics (kcat/Km) of purified Rib7 with DAROPP versus AROPP and with NADPH versus NADH, to quantify substrate and cofactor preference in vivo-relevant terms.
Diaminohydroxyphoshoribosylaminopyrimidine deaminase; catalyzes the second step of the riboflavin biosynthesis pathway
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