Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyRibulose-phoshate binding barrel 8042359 3000216 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyRibulose-phoshate binding barrel 8042359 3000216 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ARibul_P_3_epime1h1zA1 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: Ribul_P_3_epimECOD (1.6)
BRibul_P_3_epime1h1zB1 A: a/b barrelsX: TIM beta/alpha-barrelH: TIM barrels (From Topology)T: TIM barrelsF: Ribul_P_3_epimECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.20.20.70 Alpha Beta Alpha-Beta Barrel TIM Barrel Aldolase class ICATH (4.3.0)
B3.20.20.70 Alpha Beta Alpha-Beta Barrel TIM Barrel Aldolase class ICATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B
PF00834Ribulose-phosphate 3 epimerase family (Ribul_P_3_epim)Ribulose-phosphate 3 epimerase familyThis enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B
D-RIBULOSE-5-PHOSPHATE 3-EPIMERASE

InterPro: Protein Family Classification InterPro Database Homepage

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

ChainsEnzyme NameDescriptionCatalytic Residues
ribulose-phosphate 3-epimerase (cytoplasmic)  M-CSA #270

Ribulose-phosphate 3-epimerase (EC:5.1.3.1) (also known as RPE, pentose-5-phosphate 3-epimerase or PPE) is the enzyme that converts D-ribulose 5-phosphate (Ru5P) into D-xylulose 5-phosphate in Calvin's reductive pentose phosphate cycle. RPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues and have a TIM barrel structure.

This enzyme participates in both the oxidative and reductive pentose phosphate pathways and is thus an amphibolic enzyme [PMID:12547196]. There is some discussion as to whether this enzyme is zinc dependent or not. No zinc dependence has been reported [PMID:12547196]. The zinc independent (in which a water molecule is bound in place of a zinc ion to the two histidine residues that are seen as the zinc binding ligands as well as the two catalytic aspartate residues) mechanism has issues relating to how the intermediate formed is stabilised, and it has been suggested that the three strictly conserved methionines (Met40, Met71 and Met144) act as a transient 'electrostatic cushion' [PMID:10191144]. However, the alternative in which the zinc ion stabilises the oxyanion formed is more attractive [PMID:12547196] with the methionine residues aiding in this process and ensuring a hydrophobic and thus proton free environment. The actual mechanisms (with respect to the bonds formed and cleaved) are identical between the two proposals, the only difference lies in how the intermediate is stabilised [PMID:10191144, PMID:12547196, PMID:15333955].

Defined by 8 residues: SER:A-12 [auth A-11]HIS:A-37 [auth A-36]ASP:A-39 [auth A-38]MET:A-41 [auth A-40]HIS:A-70 [auth A-69]MET:A-72 [auth A-71]MET:A-145 [auth A-144]ASP:A-179 [auth A-178]
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