3DDO | pdb_00003ddo

X-RAY Structure of the Uridine Phosphorylase from Salmonella Typhimurium in Complex with by Phosphate Ion at 1.5A Resolution

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)
B	d3ddob_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
C	d3ddoc_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
D	d3ddod_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
F	d3ddof_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
E	d3ddoe_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	SCOPe (2.08)
A	d3ddoa_	Alpha and beta proteins (a/b)	Phosphorylase/hydrolase-like	Purine and uridine phosphorylases	Purine and uridine phosphorylases	Uridine phosphorylase	(Salmonella enterica subsp. enterica serovar Typhimurium ) [TaxId: 90371 ],	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	8042334	3000626	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Purine and uridine phosphorylases	8042334	3000626	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Purine and uridine phosphorylases	8042334	3000626	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Purine and uridine phosphorylases	8042334	3000626	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Purine and uridine phosphorylases	8042334	3000626	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Purine and uridine phosphorylases	8042334	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	BPL_C	e3ddoB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: BPL_C	ECOD (v294.1)
C	BPL_C	e3ddoC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: BPL_C	ECOD (v294.1)
D	BPL_C	e3ddoD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: BPL_C	ECOD (v294.1)
F	BPL_C	e3ddoF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: BPL_C	ECOD (v294.1)
E	BPL_C	e3ddoE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: BPL_C	ECOD (v294.1)
A	Abhydrolase_3	e3ddoA1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: alpha/beta-Hydrolases	T: alpha/beta-Hydrolases	F: Abhydrolase_3	ECOD (v294.1)

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)
C	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase 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)
F	3.40.50.1580	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nucleoside phosphorylase 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)
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, 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

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	Uridine phosphorylase	pentosyltransferase activity glycosyltransferase activity uridine phosphorylase activity transferase activity catalytic activity pyrimidine-nucleoside phosphorylase activity	ribose phosphate metabolic process nucleotide biosynthetic process pyrimidine ribonucleotide salvage carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine-containing compound salvage nucleobase-containing compound metabolic process pyrimidine nucleotide salvage nucleotide salvage metabolic compound salvage ribonucleotide biosynthetic process UMP salvage UMP biosynthetic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process ribose phosphate metabolic process nucleotide biosynthetic process pyrimidine ribonucleotide salvage carbohydrate derivative metabolic process pyrimidine nucleotide metabolic process pyrimidine-containing compound salvage nucleobase-containing compound metabolic process pyrimidine nucleotide salvage nucleotide salvage metabolic compound salvage ribonucleotide biosynthetic process UMP salvage UMP biosynthetic process ribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process UMP metabolic process small molecule metabolic process pyrimidine-containing compound biosynthetic process phosphorus metabolic process nucleoside monophosphate metabolic process ribose phosphate biosynthetic process pyrimidine ribonucleotide metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process pyrimidine nucleoside monophosphate metabolic process pyrimidine ribonucleoside monophosphate metabolic process pyrimidine-containing compound metabolic process primary metabolic process nucleobase-containing compound biosynthetic process nucleotide metabolic process nucleoside monophosphate biosynthetic process biosynthetic process pyrimidine ribonucleoside monophosphate biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process metabolic process cellular process pyrimidine nucleoside monophosphate biosynthetic process ribonucleoside monophosphate biosynthetic process pyrimidine nucleotide biosynthetic process pyrimidine ribonucleotide biosynthetic process carbohydrate derivative catabolic process catabolic process glycosyl compound catabolic process nucleoside metabolic process nucleobase-containing compound catabolic process nucleobase-containing small molecule catabolic process nucleoside catabolic process small molecule catabolic process organophosphate catabolic process nucleoside phosphate catabolic process nucleotide catabolic 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	IPR018016	Nucleoside phosphorylase, conserved site	Conserved Site
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	IPR010058	Uridine phosphorylase	Family
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.