1TPT

THREE-DIMENSIONAL STRUCTURE OF THYMIDINE PHOSPHORYLASE FROM ESCHERICHIA COLI AT 2.8 ANGSTROMS RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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	d1tpta1	All alpha proteins	Methionine synthase domain-like	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Thymidine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1tpta2	Alpha and beta proteins (a/b)	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Thymidine phosphorylase	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1tpta3	Alpha and beta proteins (a+b)	alpha/beta-Hammerhead	Pyrimidine nucleoside phosphorylase C-terminal domain	Pyrimidine nucleoside phosphorylase C-terminal domain	Thymidine 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)
A	SCOP2B Superfamily	Pyrimidine nucleoside phosphorylase C-terminal domain	8035018	3000876	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	8044211	3001630	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	8037570	3000348	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	Glycos_trans_3N	e1tptA1	A: alpha arrays	X: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)	T: Nucleoside phosphorylase/phosphoribosyltransferase-N	F: Glycos_trans_3N	ECOD (1.6)
A	PYNP_C	e1tptA2	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: PYNP_C	ECOD (1.6)
A	Glycos_transf_3	e1tptA3	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: Glycos_transf_3	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	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	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	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular 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 primary metabolic process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular 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 primary metabolic process glycosyl compound metabolic process carbohydrate derivative metabolic process pyrimidine nucleoside metabolic process nucleoside metabolic process deoxyribonucleoside metabolic process thymidine metabolic process pyrimidine deoxyribonucleoside metabolic process	cellular anatomical structure membrane intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000053	Thymidine/pyrimidine-nucleoside phosphorylase	Family
A	IPR035902	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily	Homologous Superfamily
A	IPR036320	Glycosyl transferase family 3, N-terminal domain superfamily	Homologous Superfamily
A	IPR013465	Thymidine phosphorylase	Family
A	IPR036566	Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily	Homologous Superfamily
A	IPR000312	Glycosyl transferase, family 3	Domain
A	IPR017872	Pyrimidine-nucleoside phosphorylase, conserved site	Conserved Site
A	IPR017459	Glycosyl transferase family 3, N-terminal domain	Domain
A	IPR013102	Pyrimidine nucleoside phosphorylase, C-terminal	Domain
A	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.