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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad1azya1 All alpha proteins Methionine synthase domain-like Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Thymidine phosphorylase (Escherichia coli K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Ad1azya2 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 K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Ad1azya3 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 K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Ad1azya4 Artifacts Tags Tags Tags N-terminal Tags (Escherichia coli K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Bd1azyb1 All alpha proteins Methionine synthase domain-like Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain Thymidine phosphorylase (Escherichia coli K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Bd1azyb2 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 K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Bd1azyb3 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 K-12 ) [TaxId: 83333 ], SCOPe (2.08)
Bd1azyb4 Artifacts Tags Tags Tags N-terminal Tags (Escherichia coli K-12 ) [TaxId: 83333 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyNucleoside phosphorylase/phosphoribosyltransferase catalytic domain 8044211 3001630 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyNucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 8037570 3000348 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyPyrimidine nucleoside phosphorylase C-terminal domain 8035018 3000876 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyPyrimidine nucleoside phosphorylase C-terminal domain 8035018 3000876 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyNucleoside phosphorylase/phosphoribosyltransferase N-terminal domain 8037570 3000348 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyNucleoside phosphorylase/phosphoribosyltransferase catalytic domain 8044211 3001630 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AGlycos_trans_3Ne1azyA1 A: alpha arraysX: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)T: Nucleoside phosphorylase/phosphoribosyltransferase-NF: Glycos_trans_3NECOD (1.6)
APYNP_Ce1azyA2 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Pyrimidine nucleoside phosphorylase C-terminal domainF: PYNP_CECOD (1.6)
AGlycos_transf_3e1azyA3 A: a/b three-layered sandwichesX: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)H: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)T: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domainF: Glycos_transf_3ECOD (1.6)
BGlycos_trans_3Ne1azyB1 A: alpha arraysX: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)H: Nucleoside phosphorylase/phosphoribosyltransferase-N (From Topology)T: Nucleoside phosphorylase/phosphoribosyltransferase-NF: Glycos_trans_3NECOD (1.6)
BPYNP_Ce1azyB2 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Pyrimidine nucleoside phosphorylase C-terminal domainF: PYNP_CECOD (1.6)
BGlycos_transf_3e1azyB3 A: a/b three-layered sandwichesX: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)H: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain (From Topology)T: Nucleoside phosphorylase/phosphoribosyltransferase catalytic domainF: Glycos_transf_3ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B
PF00591Glycosyl transferase family, a/b domain (Glycos_transf_3)Glycosyl transferase family, a/b domain- Family
A, B
PF02885Glycosyl transferase family, helical bundle domain (Glycos_trans_3N)Glycosyl transferase family, helical bundle domainThis family includes anthranilate phosphoribosyltransferase (TrpD), thymidine phosphorylase. All these proteins can transfer a phosphorylated ribose substrate.Domain
A, B
PF07831Pyrimidine nucleoside phosphorylase C-terminal domain (PYNP_C)Pyrimidine nucleoside phosphorylase C-terminal domainThis 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B
THYMIDINE PHOSPHORYLASE

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

ChainsEnzyme NameDescriptionCatalytic Residues
thymidine phosphorylase  M-CSA #413

Thymidine phosphorylases (TP) are key enzymes in nucleoside metabolism. In the presence of inorganic phosphate, they catalyse the reversible phosphorolysis of the glycosidic bond in thymidine- and uridine-2′-deoxyribosides, with the formation of free base and deoxyribose 1-phosphate. In addition to phosphorolysis, they also catalyse the transfer of the deoxyribosyl moiety from one pyrimidine base to another. This transglycosylation reaction plays a key role in the salvage pathway of nucleoside biosyntheses, providing an alternative to the de novo purine and pyrimidine biosynthetic pathways.

There are two families of nucleoside phosphorylases, which differ remarkably in the type of quaternary structure and in polypeptide chain folding. TP belongs to the family II nucleoside phosphorylases which comprises all pyrimidine phosphorylases (PyNPs) except for uridine phosphorylase. All bacterial and mammalian pyrimidine phosphorylases of family II display a dimeric quaternary structure with subunits consisting of a small alpha domain separated by a large cleft from a larger alpha/beta domain. The biologically active form of these enzymes is a dimer.

Mammalian thymidine phosphorylases stimulate tumour growth, and their level is enhanced in tumour cells, where they are involved in angiogenesis and development of metastasis. Owing to their ability to catalyse transglycosylation, some bacterial TPs are widely used in biotechnology for the large-scale production of natural 2′-deoxy-beta-D-ribonucleosides and their analogues containing modifications in the carbohydrate and base fragments. Among these nucleosides are many biologically important compounds with anticancer and antiviral activity. Therefore, the search for compounds which are able to regulate or inhibit TP activity as well as study of the interactions of these compounds with TP is of special interest. Knowledge at the atomic level of the interaction of such compounds with TP and other enzymes of nucleoside metabolism is required for the rational design of new drugs and the engineering of new forms of the enzymes with altered selectivity.

Defined by 9 residues: ASP:A-83LYS:A-84HIS:A-85SER:A-86THR:A-123ARG:A-171SER:A-186LYS:A-190LYS:A-191
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