5UMF | pdb_00005umf

Crystal Structure of a Ribulose-phosphate 3-epimerase from Neisseria gonorrhoeae with bound phosphate

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C	d5umfc_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Neisseria gonorrhoeae NCCP11945 ) [TaxId: 521006 ],	SCOPe (2.08)
B	d5umfb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Neisseria gonorrhoeae NCCP11945 ) [TaxId: 521006 ],	SCOPe (2.08)
A	d5umfa_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Ribulose-phoshate binding barrel	automated matches	automated matches	(Neisseria gonorrhoeae NCCP11945 ) [TaxId: 521006 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8083105	3000216	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribulose-phoshate binding barrel	8083105	3000216	SCOP2B (2022-06-29)
A	SCOP2 Family	D-ribulose-5-phosphate 3-epimerase	8083104	4003059	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ribulose-phoshate binding barrel	8083105	3000216	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	Ribul_P_3_epim	e5umfC1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Ribul_P_3_epim	ECOD (1.6)
B	Ribul_P_3_epim	e5umfB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Ribul_P_3_epim	ECOD (1.6)
A	Ribul_P_3_epim	e5umfA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Ribul_P_3_epim	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	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)
A	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, C	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, C	Ribulose-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	nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process carbohydrate derivative metabolic process primary metabolic process generation of precursor metabolites and energy glucose 6-phosphate metabolic process nucleotide metabolic process NADP+ metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process NADPH regeneration purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process pentose-phosphate shunt nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process carbohydrate derivative metabolic process primary metabolic process generation of precursor metabolites and energy glucose 6-phosphate metabolic process nucleotide metabolic process NADP+ metabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process NADPH regeneration purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process pentose-phosphate shunt phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process carbohydrate metabolic process biosynthetic process photosynthesis reductive pentose-phosphate cycle carbohydrate biosynthetic process photosynthesis, dark reaction carbon fixation monosaccharide metabolic process catabolic process carbohydrate catabolic process monosaccharide catabolic process small molecule catabolic process pentose metabolic process pentose catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.