1H1Z

The structure of the cytosolic D-ribulose-5-phosphate 3-epimerase from rice complexed with sulfate and zinc

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1h1za_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	D-ribulose-5-phosphate 3-epimerase	D-ribulose-5-phosphate 3-epimerase	RICE (Oryza sativa ) [TaxId: 4530 ],	SCOPe (2.08)
B	d1h1zb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	D-ribulose-5-phosphate 3-epimerase	D-ribulose-5-phosphate 3-epimerase	RICE (Oryza sativa ) [TaxId: 4530 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8042359	3000216	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8042359	3000216	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PF00834	e1h1zA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00834	ECOD (1.6)
B	PF00834	e1h1zB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00834	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00834	Ribulose-phosphate 3 epimerase family (Ribul_P_3_epim)	Ribulose-phosphate 3 epimerase family	This enzyme catalyses the conversion of D-ribulose 5-phosphate into D-xylulose 5-phosphate.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	D-RIBULOSE-5-PHOSPHATE 3-EPIMERASE	isomerase activity racemase and epimerase activity D-ribulose-phosphate 3-epimerase activity racemase and epimerase activity, acting on carbohydrates and derivatives catalytic activity cation binding ion binding binding metal ion binding small molecule binding	carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process ribose phosphate metabolic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process glucose 6-phosphate metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process cellular aldehyde metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process ribose phosphate metabolic process carbohydrate derivative metabolic process glyceraldehyde-3-phosphate metabolic process glucose 6-phosphate metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process nucleobase-containing small molecule metabolic process cellular aldehyde metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process pyridine-containing compound metabolic process small molecule metabolic process phosphorus metabolic process pyridine nucleotide metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process organonitrogen compound metabolic process cellular metabolic process generation of precursor metabolites and energy nucleotide metabolic process purine-containing compound metabolic process NADP metabolic process organic cyclic compound metabolic process NADPH regeneration organophosphate metabolic process cellular process pentose-phosphate shunt, non-oxidative branch	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000056	Ribulose-phosphate 3-epimerase-like	Family
A, B	IPR011060	Ribulose-phosphate binding barrel	Homologous Superfamily
A, B	IPR026019	Ribulose-phosphate 3-epimerase	Family
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	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] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 5.1.3.1 (PDB Primary Data) Search M-CSA Motif + EC 5.1.3.1

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.