3MKM | pdb_00003mkm

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK (Apo-form)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
D	d3mkmd_	Alpha and beta proteins (a/b)	Nucleoside hydrolase	Nucleoside hydrolase	Nucleoside hydrolase	Pyrimidine nucleoside hydrolase YeiK	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3mkmc_	Alpha and beta proteins (a/b)	Nucleoside hydrolase	Nucleoside hydrolase	Nucleoside hydrolase	Pyrimidine nucleoside hydrolase YeiK	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3mkmb_	Alpha and beta proteins (a/b)	Nucleoside hydrolase	Nucleoside hydrolase	Nucleoside hydrolase	Pyrimidine nucleoside hydrolase YeiK	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3mkma_	Alpha and beta proteins (a/b)	Nucleoside hydrolase	Nucleoside hydrolase	Nucleoside hydrolase	Pyrimidine nucleoside hydrolase YeiK	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	IU_nuc_hydro	e3mkmD1	A: a/b three-layered sandwiches	X: Nucleoside hydrolase (From Topology)	H: Nucleoside hydrolase (From Topology)	T: Nucleoside hydrolase	F: IU_nuc_hydro	ECOD (1.6)
C	IU_nuc_hydro	e3mkmC1	A: a/b three-layered sandwiches	X: Nucleoside hydrolase (From Topology)	H: Nucleoside hydrolase (From Topology)	T: Nucleoside hydrolase	F: IU_nuc_hydro	ECOD (1.6)
B	IU_nuc_hydro	e3mkmB1	A: a/b three-layered sandwiches	X: Nucleoside hydrolase (From Topology)	H: Nucleoside hydrolase (From Topology)	T: Nucleoside hydrolase	F: IU_nuc_hydro	ECOD (1.6)
A	IU_nuc_hydro	e3mkmA1	A: a/b three-layered sandwiches	X: Nucleoside hydrolase (From Topology)	H: Nucleoside hydrolase (From Topology)	T: Nucleoside hydrolase	F: IU_nuc_hydro	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.245.10	Alpha Beta	Alpha-Beta Complex	Inosine-uridine Nucleoside N-ribohydrolase	Chain A	CATH (4.3.0)
C	3.90.245.10	Alpha Beta	Alpha-Beta Complex	Inosine-uridine Nucleoside N-ribohydrolase	Chain A	CATH (4.3.0)
B	3.90.245.10	Alpha Beta	Alpha-Beta Complex	Inosine-uridine Nucleoside N-ribohydrolase	Chain A	CATH (4.3.0)
A	3.90.245.10	Alpha Beta	Alpha-Beta Complex	Inosine-uridine Nucleoside N-ribohydrolase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01156	Inosine-uridine preferring nucleoside hydrolase (IU_nuc_hydro)	Inosine-uridine preferring nucleoside hydrolase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Putative uncharacterized protein YeiK	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding hydrolase activity, acting on glycosyl bonds purine nucleosidase activity hydrolase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity uridine nucleosidase activity ribosylpyrimidine nucleosidase activity	carbohydrate derivative catabolic process catabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process primary metabolic process glycosyl compound catabolic process purine-containing compound catabolic process nucleoside metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule catabolic process nucleobase-containing small molecule metabolic process nucleoside catabolic process carbohydrate derivative catabolic process catabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process primary metabolic process glycosyl compound catabolic process purine-containing compound catabolic process nucleoside metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule catabolic process nucleobase-containing small molecule metabolic process nucleoside catabolic process small molecule metabolic process metabolic process cellular process small molecule catabolic process purine nucleoside metabolic process pyrimidine nucleobase metabolic process pyrimidine-containing compound metabolic process nucleobase metabolic process pyrimidine-containing compound catabolic process pyrimidine nucleoside metabolic process pyrimidine nucleoside catabolic process pyrimidine ribonucleoside metabolic process pyrimidine ribonucleoside catabolic process ribonucleoside catabolic process ribonucleoside metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR036452	Ribonucleoside hydrolase-like	Homologous Superfamily
A, B, C, D	IPR015910	Inosine/uridine-preferring nucleoside hydrolase, conserved site	Conserved Site
A, B, C, D	IPR023186	Inosine/uridine-preferring nucleoside hydrolase	Family
A, B, C, D	IPR022977	Pyrimidine-specific ribonucleoside hydrolase RihB	Family
A, B, C, D	IPR001910	Inosine/uridine-preferring nucleoside hydrolase domain	Domain

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.