RPE1

UniProt ID: P46969
Organism: Saccharomyces cerevisiae S288C
Review Status: DRAFT
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Gene Description

Rpe1 (YJL121C; POS18) is the sole D-ribulose-5-phosphate 3-epimerase (EC 5.1.3.1) of Saccharomyces cerevisiae. It is a cytosolic TIM-barrel enzyme of the RPE family that interconverts D-ribulose 5-phosphate and D-xylulose 5-phosphate in the non-oxidative pentose phosphate pathway, supplying xylulose 5-phosphate to transketolase. Like its human orthologue, it is predicted to bind one divalent metal ion per subunit. rpe1 deletion mutants lack epimerase activity and cannot grow on D-xylulose. rpe1 (pos18) mutants were isolated as hydrogen-peroxide-sensitive, consistent with a role for PPP flux in NADPH-dependent oxidative-stress protection.

Existing Annotations Review

GO Term Evidence Action Reason
GO:0004750 D-ribulose-phosphate 3-epimerase activity
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA from RPE node PTN000202667 (donors include fly, mouse, rat, fission yeast and Rpe1 itself). Rpe1 is the sole ribulose-phosphate 3-epimerase of S. cerevisiae.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
PMID:8929392
Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose.
GO:0004750 D-ribulose-phosphate 3-epimerase activity
IDA
PMID:8929392
Cloning and characterization of the first two genes of the n... 		ACCEPT
Summary: Miosga and Zimmermann measured high RPE activity in crude extracts, dependent on RPE1 (none in rpe1 deletions).
Supporting Evidence:
PMID:8929392
Rpe1p has an unexpected high specific activity of 2148 mU x (mg protein)-1 in crude extracts.
PMID:8929392
Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose.
GO:0004750 D-ribulose-phosphate 3-epimerase activity
IEA
GO_REF:0000120 		ACCEPT
Summary: EC 5.1.3.1 / RHEA:13677 and InterPro IPR026019 mapped to ribulose-phosphate 3-epimerase activity. Correct.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
GO:0004750 D-ribulose-phosphate 3-epimerase activity
IMP
PMID:8929392
Cloning and characterization of the first two genes of the n... 		ACCEPT
Summary: rpe1 deletion mutants lack ribulose-5-phosphate 3-epimerase activity and cannot grow on D-xylulose. Juhnke et al. independently found no RPE activity in the pos18 (rpe1) mutant.
Supporting Evidence:
PMID:8929392
Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose.
PMID:8879247
No detectable ribulose 5-phosphate epimerase activity was found in the pos18 mutant, suggesting that the corresponding structural gene is affected in this mutant.
GO:0004750 D-ribulose-phosphate 3-epimerase activity
ISS
GO_REF:0000024 		ACCEPT
Summary: Sequence-similarity transfer from human RPE (Q96AT9). Consistent with the yeast mutant data.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
PMID:8929392
Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose.
GO:0004750 D-ribulose-phosphate 3-epimerase activity
RCA
GO_REF:0000123 		ACCEPT
Summary: YeastPathways RCA (NONOXIPENT-PWY) assigning ribulose-5-phosphate <-> xylulose-5-phosphate (EC 5.1.3.1) to Rpe1. Correct.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
PMID:8929392
Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose.
GO:0004750 D-ribulose-phosphate 3-epimerase activity
RCA
GO_REF:0000123 		ACCEPT
Summary: YeastPathways RCA (PENTOSE-P-PWY) assigning ribulose-5-phosphate <-> xylulose-5-phosphate (EC 5.1.3.1) to Rpe1. Correct.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
PMID:8929392
Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose.
GO:0005737 cytoplasm
IEA
GO_REF:0000044 		ACCEPT
Summary: UniProt subcellular-location mapping (SL-0086 Cytoplasm) for Rpe1. Correct, though the enzyme is cytosolic.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
SUBCELLULAR LOCATION: Cytoplasm.
GO:0005829 cytosol
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA (PTN000202667; donors mouse Rpe and E. coli Rpe) placing RPE as active in the cytosol. Correct.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
GO:0005829 cytosol
RCA
GO_REF:0000123 		ACCEPT
Summary: YeastPathways RCA (NONOXIPENT-PWY) placing the epimerase step in the cytosol. Correct.
Supporting Evidence:
PMID:11298766
unravelling of the network of active central pathways in cytosol and mitochondria
GO:0005829 cytosol
RCA
GO_REF:0000123 		ACCEPT
Summary: YeastPathways RCA (PENTOSE-P-PWY) placing the epimerase step in the cytosol. Correct.
Supporting Evidence:
PMID:11298766
unravelling of the network of active central pathways in cytosol and mitochondria
GO:0005829 cytosol
TAS
PMID:11298766
Central carbon metabolism of Saccharomyces cerevisiae explor... 		ACCEPT
Summary: Maaheimo et al. used 13C fractional labelling to resolve cytosolic and mitochondrial central-carbon fluxes in yeast; the pentose phosphate pathway operates in the cytosol and serves biosynthesis. The curator's TAS for a cytosolic Rpe1 is reasonable.
Supporting Evidence:
PMID:11298766
unravelling of the network of active central pathways in cytosol and mitochondria
PMID:11298766
the pentose phosphate pathways serve for biosynthesis only
GO:0005975 carbohydrate metabolic process
IBA
GO_REF:0000033 		KEEP AS NON CORE
Summary: PAINT IBA at node PTN000202667, whose donors include E. coli AlsE-like (P32719) and Rpe proteins acting on different phosphosugars. This explains the generic 'carbohydrate metabolic process'. It is correct but uninformative for Rpe1, whose specific process (non-oxidative PPP) is annotated separately.
Reason: Generic family-level BP from a deep node spanning several epimerase specificities; true but non-specific.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
GO:0005975 carbohydrate metabolic process
IEA
GO_REF:0000002 		MODIFY
Summary: InterPro IPR000056 (ribulose-phosphate binding barrel, RPE-like) mapped to carbohydrate metabolic process. Correct but too general.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
PMID:8929392
Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose.
GO:0006098 pentose-phosphate shunt
IEA
GO_REF:0000120 		ACCEPT
Summary: UniPathway UPA00115 / InterPro IPR026019 mapping to pentose-phosphate shunt. Correct; the more precise non-oxidative-branch term is also present.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
PATHWAY: Carbohydrate degradation; pentose phosphate pathway; D-
GO:0006098 pentose-phosphate shunt
IMP
PMID:8929392
Cloning and characterization of the first two genes of the n... 		ACCEPT
Summary: rpe1 deletion abolishes RPE activity and growth on D-xylulose, so Rpe1 acts in the pentose phosphate pathway. Juhnke et al. also found PPP mutants including rpe1 hypersensitive to H2O2.
Supporting Evidence:
PMID:8929392
Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose.
PMID:8879247
No detectable ribulose 5-phosphate epimerase activity was found in the pos18 mutant, suggesting that the corresponding structural gene is affected in this mutant.
GO:0006098 pentose-phosphate shunt
RCA
GO_REF:0000123 		ACCEPT
Summary: YeastPathways RCA (PENTOSE-P-PWY) for the pentose-phosphate shunt. Correct.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
GO:0008270 zinc ion binding
RCA
PMID:30358795
The cellular economy of the Saccharomyces cerevisiae zinc pr... 		KEEP AS NON CORE
Summary: Wang et al. assigned Rpe1 to the predicted yeast zinc proteome by domain/motif searches (RCA). RPE enzymes bind one divalent metal per subunit, and the human orthologue is active with Co2+, Fe2+, Mn2+ or Zn2+. Which metal Rpe1 uses in vivo is not established, so 'zinc ion binding' is plausible but uncertain.
Reason: Computational metal-site prediction; metal identity in vivo is unresolved.
Supporting Evidence:
PMID:30358795
The yeast zinc proteome of 582 known or potential zinc-binding proteins was identified using a bioinformatics analysis that combined global domain searches with local motif searches.
file:yeast/RPE1/RPE1-uniprot.txt
Note=Binds 1 divalent metal cation per subunit. Active with Co(2+),
GO:0009052 pentose-phosphate shunt, non-oxidative branch
IBA
GO_REF:0000033 		ACCEPT
Summary: PAINT IBA (PTN000202667) for the non-oxidative PPP branch. This is Rpe1's core process.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
PMID:8929392
Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose.
GO:0009052 pentose-phosphate shunt, non-oxidative branch
RCA
GO_REF:0000123 		ACCEPT
Summary: YeastPathways RCA (NONOXIPENT-PWY) for the non-oxidative PPP branch. Correct.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
PMID:8929392
Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose.
GO:0016857 racemase and epimerase activity, acting on carbohydrates and derivatives
IEA
GO_REF:0000002 		MODIFY
Summary: InterPro IPR000056 (RPE-like family) mapped to the grouping term 'racemase and epimerase activity, acting on carbohydrates'. Correct but too general; the specific activity is well established.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
PMID:8929392
Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose.
GO:0046872 metal ion binding
IBA
GO_REF:0000033 		KEEP AS NON CORE
Summary: PAINT IBA (PTN000202667) for metal ion binding. RPE-family enzymes need one divalent metal per subunit for catalysis. Correct as a cofactor annotation, but not the core function.
Reason: Cofactor binding; true for the family, not the core activity.
Supporting Evidence:
file:yeast/RPE1/RPE1-uniprot.txt
Note=Binds 1 divalent metal cation per subunit. Active with Co(2+),

Core Functions

Ribulose-phosphate 3-epimerase interconverting D-ribulose 5-phosphate and D-xylulose 5-phosphate in the cytosolic non-oxidative pentose phosphate pathway, feeding transketolase.

Molecular Function:
D-ribulose-phosphate 3-epimerase activity
Directly Involved In:
pentose-phosphate shunt, non-oxidative branch
Cellular Locations:
cytosol
Supporting Evidence:
  • file:yeast/RPE1/RPE1-uniprot.txt
    Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
  • PMID:8929392
    Deletion mutants of RPE1 show no enzyme activity and are unable to grow on D-xylulose.
  • PMID:8929392
    Rpe1p has an unexpected high specific activity of 2148 mU x (mg protein)-1 in crude extracts.
  • PMID:8879247
    No detectable ribulose 5-phosphate epimerase activity was found in the pos18 mutant, suggesting that the corresponding structural gene is affected in this mutant.

References

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Suggested Questions for Experts

Q: Which divalent metal (Fe2+, Zn2+ or Mn2+) occupies the Rpe1 active site in vivo, and is Rpe1 inactivated by H2O2 through metal oxidation, as reported for bacterial RPE?

Deep Research

SGD

(RPE1-deep-research-sgd.md)
SGD gene description for RPE1 (yeast) SGD

SGD gene description for RPE1 (yeast)

D-ribulose-5-phosphate 3-epimerase; catalyzes a reaction in the non-oxidative part of the pentose-phosphate pathway; mutants are sensitive to oxidative stress

📚 Additional Documentation

Notes

(RPE1-notes.md)

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