3DF9

Crystal structure of E. coli MTA/SAH nucleosidase in complex with BnT-DADMeImmA

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3df9a1	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d3df9a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d3df9b_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	automated matches	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Purine and uridine phosphorylases	8098425	4000573	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Purine and uridine phosphorylases	8098426	3000626	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Purine and uridine phosphorylases	8098426	3000626	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	PF01048	e3df9A1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PF01048	ECOD (1.6)
B	PF01048	e3df9B1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PF01048	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
B	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01048	Phosphorylase superfamily (PNP_UDP_1)	Phosphorylase superfamily	Members of this family include: purine nucleoside phosphorylase (PNP) Uridine phosphorylase (UdRPase) 5'-methylthioadenosine phosphorylase (MTA phosphorylase)	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	MTA/SAH nucleosidase	hydrolase activity, acting on glycosyl bonds purine nucleosidase activity hydrolase activity methylthioadenosine nucleosidase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity adenosylhomocysteine nucleosidase activity	glycosyl compound metabolic process catabolic process deoxyribonucleoside metabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process purine deoxyribonucleoside catabolic process nucleobase-containing compound metabolic process cellular catabolic process organic substance metabolic process heterocycle metabolic process nucleobase-containing small molecule metabolic process purine deoxyribonucleoside metabolic process nitrogen compound metabolic process small molecule metabolic process glycosyl compound metabolic process catabolic process deoxyribonucleoside metabolic process purine nucleoside catabolic process carbohydrate derivative metabolic process purine deoxyribonucleoside catabolic process nucleobase-containing compound metabolic process cellular catabolic process organic substance metabolic process heterocycle metabolic process nucleobase-containing small molecule metabolic process purine deoxyribonucleoside metabolic process nitrogen compound metabolic process small molecule metabolic process organonitrogen compound catabolic process carbohydrate derivative catabolic process organonitrogen compound metabolic process cellular metabolic process cellular nitrogen compound metabolic process primary metabolic process glycosyl compound catabolic process purine-containing compound catabolic process aromatic compound catabolic process nucleoside metabolic process cellular nitrogen compound catabolic process organic cyclic compound catabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process organic cyclic compound metabolic process nucleobase-containing small molecule catabolic process nucleoside catabolic process heterocycle catabolic process deoxyribonucleoside catabolic process metabolic process cellular process small molecule catabolic process organic substance catabolic process purine nucleoside metabolic process cellular aromatic compound metabolic process oxoacid metabolic process cellular biosynthetic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process organic substance biosynthetic process sulfur compound metabolic process L-methionine biosynthetic process cellular metabolic compound salvage methionine biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process L-amino acid biosynthetic process methionine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid salvage amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process L-methionine salvage from methylthioadenosine proteinogenic amino acid biosynthetic process L-methionine salvage sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process S-adenosylmethionine metabolic process S-adenosylmethionine cycle L-methionine salvage from S-adenosylmethionine	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR035994	Nucleoside phosphorylase superfamily	Homologous Superfamily
A, B	IPR000845	Nucleoside phosphorylase domain	Domain
A, B	IPR010049	MTA/SAH nucleosidase	Family

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.