3K5W

Crystal structure of a Carbohydrate kinase (YjeF family)from Helicobacter pylori

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	YjeF_N	e3k5wA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: YjeF_N	ECOD (1.6)
A	Carb_kinase	e3k5wA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Ribokinase-like (From Topology)	T: Ribokinase-like	F: Carb_kinase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.10260	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	YjeF N-terminal domain	CATH (4.3.0)
A	3.40.1190.20	Alpha Beta	3-Layer(aba) Sandwich	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase	Ribokinase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01256	Carbohydrate kinase (Carb_kinase)	Carbohydrate kinase	-	Family
A	PF03853	YjeF-related protein N-terminus (YjeF_N)	YjeF-related protein N-terminus	YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases [1]. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be ...	YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases [1]. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128) [1], where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Carbohydrate kinase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity ADP-dependent NAD(P)H-hydrate dehydratase activity cation binding metal ion binding isomerase activity NAD(P)HX epimerase activity racemase and epimerase activity	nicotinamide nucleotide metabolic process nucleoside phosphate metabolic process cellular metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process nicotinamide nucleotide metabolic process nucleoside phosphate metabolic process cellular metabolic process primary metabolic process nucleotide metabolic process nucleobase-containing compound metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process metabolic process cellular process small molecule metabolic process phosphorus metabolic process pyridine nucleotide metabolic process metabolite repair	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000631	ATP/ADP-dependent (S)-NAD(P)H-hydrate dehydratase	Domain
A	IPR017953	Carbohydrate kinase, predicted, conserved site	Conserved Site
A	IPR036652	YjeF N-terminal domain superfamily	Homologous Superfamily
A	IPR029056	Ribokinase-like	Homologous Superfamily
A	IPR004443	YjeF N-terminal domain	Domain
A	IPR030677	Bifunctional NAD(P)H-hydrate repair enzyme Nnr	Family

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.