1T8S

Crystal Structure of E.coli AMP Nucleosidase complexed with formicin 5'-monophosphate

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)
A	d1t8sa_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	AMP nucleosidase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1t8sb_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	AMP nucleosidase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1t8sc_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	AMP nucleosidase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1t8sd_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	AMP nucleosidase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1t8se_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	AMP nucleosidase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1t8sf_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	AMP nucleosidase	(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	8027707	4000573	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Purine and uridine phosphorylases	8040086	3000626	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Purine and uridine phosphorylases	8040086	3000626	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Purine and uridine phosphorylases	8040086	3000626	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Purine and uridine phosphorylases	8040086	3000626	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Purine and uridine phosphorylases	8040086	3000626	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Purine and uridine phosphorylases	8040086	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	PNP_UDP_1	e1t8sA1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
B	PNP_UDP_1	e1t8sB1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
C	PNP_UDP_1	e1t8sC1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
D	PNP_UDP_1	e1t8sD1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
E	PNP_UDP_1	e1t8sE1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)
F	PNP_UDP_1	e1t8sF1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like (From Topology)	T: Peptidyl-tRNA hydrolase-like	F: PNP_UDP_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1730.10	Alpha Beta	2-Layer Sandwich	amp nucleosidase, domain 1	AMP nucleoside phosphorylase, N-terminal domain	CATH (4.3.0)
A	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
B	3.30.1730.10	Alpha Beta	2-Layer Sandwich	amp nucleosidase, domain 1	AMP nucleoside phosphorylase, N-terminal 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)
C	3.30.1730.10	Alpha Beta	2-Layer Sandwich	amp nucleosidase, domain 1	AMP nucleoside phosphorylase, N-terminal domain	CATH (4.3.0)
C	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
D	3.30.1730.10	Alpha Beta	2-Layer Sandwich	amp nucleosidase, domain 1	AMP nucleoside phosphorylase, N-terminal domain	CATH (4.3.0)
D	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
E	3.30.1730.10	Alpha Beta	2-Layer Sandwich	amp nucleosidase, domain 1	AMP nucleoside phosphorylase, N-terminal domain	CATH (4.3.0)
E	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase domain	CATH (4.3.0)
F	3.30.1730.10	Alpha Beta	2-Layer Sandwich	amp nucleosidase, domain 1	AMP nucleoside phosphorylase, N-terminal domain	CATH (4.3.0)
F	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, C, D, E A, B, C, D, E, F	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
A, B, C, D, E A, B, C, D, E, F	PF10423	Bacterial AMP nucleoside phosphorylase N-terminus (AMNp_N)	Bacterial AMP nucleoside phosphorylase N-terminus	This is the N-terminal domain of bacterial AMP nucleoside phosphorylase (AMNp). The N- and C-termini form distinct domains which intertwine with each other to form a stable monomer which associates with five other monomers to yield the active hexamer ...	This is the N-terminal domain of bacterial AMP nucleoside phosphorylase (AMNp). The N- and C-termini form distinct domains which intertwine with each other to form a stable monomer which associates with five other monomers to yield the active hexamer. The N-terminus consists of a long helix and a four-stranded sheet with a novel topology. The C-terminus binds the nucleoside whereas the N-terminus acts as the enzymatic regulatory domain. AMNp (EC:3.2.2.4) catalyses the hydrolysis of AMP to form adenine and ribose 5-phosphate. thereby regulating intracellular AMP levels [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	AMP nucleosidase	hydrolase activity, acting on glycosyl bonds AMP nucleosidase activity hydrolase activity hydrolase activity, hydrolyzing N-glycosyl compounds catalytic activity	ribose phosphate metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process AMP metabolic process nucleobase-containing compound metabolic process nucleotide salvage ribonucleotide biosynthetic process purine nucleoside monophosphate biosynthetic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process ribose phosphate metabolic process purine ribonucleoside monophosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process purine ribonucleotide biosynthetic process AMP metabolic process nucleobase-containing compound metabolic process nucleotide salvage ribonucleotide biosynthetic process purine nucleoside monophosphate biosynthetic process purine ribonucleoside monophosphate metabolic process purine nucleotide metabolic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process purine nucleoside monophosphate metabolic process phosphate-containing compound metabolic process purine nucleotide salvage AMP salvage small molecule metabolic process phosphorus metabolic process ribose phosphate biosynthetic process cellular metabolic compound salvage nucleoside monophosphate metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process purine-containing compound salvage primary metabolic process nucleotide metabolic process nucleobase-containing compound biosynthetic process nucleoside monophosphate biosynthetic process purine-containing compound metabolic process biosynthetic process purine ribonucleotide salvage organophosphate metabolic process organophosphate biosynthetic process AMP biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process purine ribonucleotide metabolic process ribonucleoside monophosphate biosynthetic process purine nucleotide biosynthetic process glycosyl compound metabolic process nucleoside 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, E A, B, C, D, E, F	IPR047039	AMP nucleosidase, phosphorylase domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR011271	AMP nucleosidase	Family
A, B, C, D, E A, B, C, D, E, F	IPR035994	Nucleoside phosphorylase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR037109	AMP nucleoside phosphorylase, N-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR018953	AMP nucleoside phosphorylase, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR000845	Nucleoside phosphorylase 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.