1BRW

THE CRYSTAL STRUCTURE OF PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE IN A CLOSED CONFORMATION

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)
A	d1brwa1	All alpha proteins	Methionine synthase domain-like	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Pyrimidine nucleoside phosphorylase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
A	d1brwa2	Alpha and beta proteins (a/b)	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Pyrimidine nucleoside phosphorylase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
A	d1brwa3	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	Pyrimidine nucleoside phosphorylase C-terminal domain	Pyrimidine nucleoside phosphorylase C-terminal domain	Pyrimidine nucleoside phosphorylase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d1brwb1	All alpha proteins	Methionine synthase domain-like	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Pyrimidine nucleoside phosphorylase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d1brwb2	Alpha and beta proteins (a/b)	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Pyrimidine nucleoside phosphorylase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)
B	d1brwb3	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	Pyrimidine nucleoside phosphorylase C-terminal domain	Pyrimidine nucleoside phosphorylase C-terminal domain	Pyrimidine nucleoside phosphorylase	(Geobacillus stearothermophilus ) [TaxId: 1422 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	8031834	4003843	SCOP2 (2022-06-29)
A	SCOP2 Family	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	8025194	4000984	SCOP2 (2022-06-29)
A	SCOP2 Family	Pyrimidine nucleoside phosphorylase C-terminal domain	8022641	4001133	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	8044212	3001630	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	8037573	3000348	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Pyrimidine nucleoside phosphorylase C-terminal domain	8035021	3000876	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	8037573	3000348	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pyrimidine nucleoside phosphorylase C-terminal domain	8035021	3000876	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	8044212	3001630	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	PF02885	e1brwA1	A: alpha arrays	X: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase-N	F: PF02885	ECOD (1.6)
A	PF07831	e1brwA2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Pyrimidine nucleoside phosphorylase C-terminal domain	F: PF07831	ECOD (1.6)
A	PF00591	e1brwA3	A: a/b three-layered sandwiches	X: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	F: PF00591	ECOD (1.6)
B	PF02885	e1brwB1	A: alpha arrays	X: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase-N	F: PF02885	ECOD (1.6)
B	PF07831	e1brwB2	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Pyrimidine nucleoside phosphorylase C-terminal domain	F: PF07831	ECOD (1.6)
B	PF00591	e1brwB3	A: a/b three-layered sandwiches	X: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	F: PF00591	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1170.30	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
A	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
A	1.20.970.10	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)
B	3.90.1170.30	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	CATH (4.3.0)
B	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
B	1.20.970.10	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00591	Glycosyl transferase family, a/b domain (Glycos_transf_3)	Glycosyl transferase family, a/b domain	-	Family
A, B	PF02885	Glycosyl transferase family, helical bundle domain (Glycos_trans_3N)	Glycosyl transferase family, helical bundle domain	This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate.	Domain
A, B	PF07831	Pyrimidine nucleoside phosphorylase C-terminal domain (PYNP_C)	Pyrimidine nucleoside phosphorylase C-terminal domain	This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [1,2]. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside ...	This domain is found at the C-terminal end of the large alpha/beta domain making up various pyrimidine nucleoside phosphorylases [1,2]. It has slightly different conformations in different members of this family. For example, in pyrimidine nucleoside phosphorylase (PYNP, Swiss:P77826) there is an added three-stranded anti-parallel beta sheet as compared to other members of the family, such as E. coli thymidine phosphorylase (TP, Swiss:P07650) [1]. The domain contains an alpha/ beta hammerhead fold and residues in this domain seem to be important in formation of the homodimer [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PROTEIN (PYRIMIDINE NUCLEOSIDE PHOSPHORYLASE)	1,4-alpha-oligoglucan phosphorylase activity glycosyltransferase activity transferase activity hexosyltransferase activity catalytic activity deoxyuridine phosphorylase activity pentosyltransferase activity pyrimidine-nucleoside phosphorylase activity thymidine phosphorylase activity uridine phosphorylase activity cation binding ion binding binding metal ion binding 1,4-alpha-oligoglucan phosphorylase activity glycosyltransferase activity transferase activity hexosyltransferase activity catalytic activity deoxyuridine phosphorylase activity pentosyltransferase activity pyrimidine-nucleoside phosphorylase activity thymidine phosphorylase activity uridine phosphorylase activity cation binding ion binding binding metal ion binding small molecule binding	organonitrogen compound metabolic process pyrimidine-containing compound metabolic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process organic cyclic compound metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process metabolic process glycosyl compound metabolic process carbohydrate derivative metabolic process pyrimidine nucleoside metabolic process organonitrogen compound metabolic process pyrimidine-containing compound metabolic process primary metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process organic cyclic compound metabolic process organic substance metabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process metabolic process glycosyl compound metabolic process carbohydrate derivative metabolic process pyrimidine nucleoside metabolic process nucleoside metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000053	Thymidine/pyrimidine-nucleoside phosphorylase	Family
A, B	IPR035902	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily	Homologous Superfamily
A, B	IPR036320	Glycosyl transferase family 3, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR036566	Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR000312	Glycosyl transferase, family 3	Domain
A, B	IPR017872	Pyrimidine-nucleoside phosphorylase, conserved site	Conserved Site
A, B	IPR017459	Glycosyl transferase family 3, N-terminal domain	Domain
A, B	IPR013102	Pyrimidine nucleoside phosphorylase, C-terminal	Domain
A, B	IPR018090	Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A	pyrimidine-nucleoside phosphorylase M-CSA #91	Pyrimidine-nucleoside phosphorylase (Py-NP) catalyses the reversible phosphorylation of both uridine and thymidine in the nucleotide synthesis salvage pathway. It is found in all lower organisms whilst in higher organisms such phosphorylases are specific to those individual nucleosides. Nevertheless, Py-NPs share 40% sequence similarity with thymidine specific phosphorylase seen in higher organisms, a prominent drug target in treating breast cancer.	Defined by 5 residues: HIS:A-82ASP:A-161ARG:A-168SER:A-183LYS:A-187 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.4.2.2 (PDB Primary Data) Search M-CSA Motif + EC 2.4.2.2

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.