4YYY | pdb_00004yyy

X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with uridine

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d4yyyb1	All alpha proteins	Methionine synthase domain-like	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	automated matches	automated matches	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)
B	d4yyyb2	Alpha and beta proteins (a/b)	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	automated matches	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)
B	d4yyyb3	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	Pyrimidine nucleoside phosphorylase C-terminal domain	automated matches	automated matches	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)
A	d4yyya1	All alpha proteins	Methionine synthase domain-like	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	automated matches	automated matches	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)
A	d4yyya2	Alpha and beta proteins (a/b)	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	automated matches	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)
A	d4yyya3	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	Pyrimidine nucleoside phosphorylase C-terminal domain	automated matches	automated matches	(Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 ) [TaxId: 99287 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e4yyyB1	A: HTH	X: HTH	H: Putative DNA-binding domain	T: Insulin	F:	ECOD (20:10:01)
A		e4yyyA1	A: HTH	X: HTH	H: Putative DNA-binding domain	T: Insulin	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.20.970.10	Mainly Alpha	Up-down Bundle	Transferase, Pyrimidine Nucleoside Phosphorylase	Chain A, 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	3.90.1170.30	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	domain 3	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)
A	3.40.1030.10	Alpha Beta	3-Layer(aba) Sandwich	Pyrimidine Nucleoside Phosphorylase	Chain A, domain 2	CATH (4.3.0)
A	3.90.1170.30	Alpha Beta	Alpha-Beta Complex	Aldehyde Oxidoreductase	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	This family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate.	Domain
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	Thymidine phosphorylase	1,4-alpha-oligoglucan phosphorylase activity glycosyltransferase activity transferase activity hexosyltransferase activity catalytic activity pentosyltransferase activity thymidine phosphorylase activity pyrimidine-nucleoside phosphorylase activity	nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process pyrimidine-containing compound metabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process deoxyribonucleoside metabolic process carbohydrate derivative metabolic process pyrimidine nucleoside metabolic process nucleoside metabolic process thymidine metabolic process nucleobase-containing compound metabolic process pyrimidine nucleobase metabolic process pyrimidine-containing compound metabolic process nucleobase-containing small molecule metabolic process nucleobase metabolic process small molecule metabolic process metabolic process cellular process primary metabolic process deoxyribonucleoside metabolic process carbohydrate derivative metabolic process pyrimidine nucleoside metabolic process nucleoside metabolic process thymidine metabolic process pyrimidine deoxyribonucleoside metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

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	IPR013465	Thymidine phosphorylase	Family
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

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.