1T0U

Crystal structure of E.coli uridine phosphorylase at 2.2 A resolution (Type-A Native)

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1t0ub_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1t0ua_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(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)
B	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	3000626	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Purine and uridine phosphorylases	8041020	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)
B	PNP_UDP_1	e1t0uB1	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)
A	PNP_UDP_1	e1t0uA1	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)
B	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase 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)

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	Uridine phosphorylase	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 cation binding potassium ion binding alkali metal ion binding metal ion binding pentosyltransferase activity glycosyltransferase activity uridine phosphorylase activity transferase activity catalytic activity pyrimidine-nucleoside phosphorylase activity identical protein binding protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process glycosyl compound metabolic process catabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process uridine metabolic process pyrimidine nucleoside metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process glycosyl compound metabolic process catabolic process pyrimidine-containing compound catabolic process carbohydrate derivative metabolic process uridine metabolic process pyrimidine nucleoside metabolic process nucleobase-containing compound metabolic process nucleobase-containing small molecule metabolic process small molecule metabolic process carbohydrate derivative catabolic process pyrimidine-containing compound metabolic process pyrimidine nucleoside catabolic process primary metabolic process glycosyl compound catabolic process nucleoside metabolic process nucleobase-containing compound catabolic process uridine catabolic process pyrimidine ribonucleoside metabolic process nucleobase-containing small molecule catabolic process nucleoside catabolic process metabolic process pyrimidine ribonucleoside catabolic process small molecule catabolic process ribonucleoside catabolic process ribonucleoside metabolic process ribose phosphate metabolic process nucleotide biosynthetic process pyrimidine ribonucleotide salvage pyrimidine nucleotide metabolic process pyrimidine-containing compound salvage pyrimidine nucleotide salvage nucleotide salvage ribonucleotide biosynthetic process UMP salvage UMP biosynthetic process ribonucleotide metabolic process ribonucleoside monophosphate metabolic process phosphate-containing compound metabolic process UMP metabolic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process ribose phosphate biosynthetic process cellular metabolic compound salvage nucleoside monophosphate metabolic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process cellular metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside monophosphate biosynthetic process biosynthetic process organophosphate metabolic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process pyrimidine ribonucleotide catabolic process ribonucleotide catabolic process pyrimidine ribonucleoside monophosphate catabolic process organophosphate catabolic process nucleoside phosphate catabolic process pyrimidine nucleotide catabolic process ribonucleoside monophosphate catabolic process nucleotide catabolic process pyrimidine nucleoside monophosphate catabolic process nucleoside monophosphate catabolic process UMP catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR035994	Nucleoside phosphorylase superfamily	Homologous Superfamily
A, B	IPR010058	Uridine phosphorylase	Family
A, B	IPR018016	Nucleoside phosphorylase, conserved site	Conserved Site
A, B	IPR000845	Nucleoside phosphorylase domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, B	uridine phosphorylase M-CSA #787	The enzyme uridine phosphorylase is very important in the pathway whereby uracil can be scavenged to increase blood uracil levels. The overall reaction thus results in the formation of ribose-1-phosphate in addition to uracil. The pathway is of particular interest because it provides a mechanism whereby the effect of base analogues such as 5BU can be minimised, thus may provide some defence against tumour formation. The enzyme itself shows significant homology to Purine nucleotide phosphorylases rather than to pyrimidine nucleotide phosphorylases, posing interesting questions about its evolution.	Defined by 4 residues: HIS:A-8GLU:A-80ARG:A-168ARG:B-223 Some residues are not modelled and lack atomic coordinates. Visualization is not available. Some residues are not modelled and lack atomic coordinates. Structure Motif searching is not available. EC: 2.4.2.3 (PDB Primary Data)

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.