Protein Domain : IPR000053

Type:  Family Name:  Thymidine/pyrimidine-nucleoside phosphorylase
Description:  Two highly similar activities are represented in this group: thymidine phosphorylase (TP, gene deoA, ) and pyrimidine-nucleoside phosphorylase (PyNP, gene pdp, ). Both are dimeric enzymes that function in the salvage pathway to catalyse the reversible phosphorolysis of pyrimidine nucleosides to the free base and sugar moieties. In the case of thymidine phosphorylase, thymidine (and to a lesser extent, 2'-deoxyuridine) is lysed to produce thymine (or uracil) and 2'-deoxyribose-1-phosphate. Pyrimidine-nucleoside phosphorylase performs the analogous reaction on thymidine (to produce the same products) and uridine (to produce uracil and ribose-1-phosphate). PyNP is typically the only pyrimidine nucleoside phosphorylase encoded by Gram positive bacteria, while eukaryotes and proteobacteria encode two: TP, and the unrelated uridine phosphorylase. In humans, TP was originally characterised as platelet-derived endothelial cell growth factor and gliostatin []. Structurally, the enzymes are homodimers, each composed of a rigid all alpha-helix lobe and a mixed alpha-helix/beta-sheet lobe, which are connected by a flexible hinge [, ]. Prior to substrate binding, the lobes are separated by a large cleft. A functional active site and subsequent catalysis occurs upon closing of the cleft. The active site, composed of a phosphate binding site and a (deoxy)ribonucleotide binding site within the cleft region, is highly conserved between the two enzymes of this group. Active site residues (Escherichia coli DeoA numbering) include the phosphate binding Lys84 and Ser86 (close to a glycine-rich loop), Ser113, and Thr123, and the pyrimidine nucleoside-binding Arg171, Ser186, and Lys190. Sequence comparison between the active site residues for both enzymes reveals only one difference [], which has been proposed to partially mediate substrate specificity. In TP, position 111 is a methionine, while the analogous position in PyNP is lysine. It should be noted that the uncharacterised archaeal members of this family differ in a number of respects from either of the characterised activities. The residue at position 108 is lysine, indicating the activity might be PyNP-like (though the determinants of substrate specificity have not been fully elucidated). Position 171 is glutamate (negative charge side chain) rather than arginine (positive charge side chain). In addition, a large loop that may "lock in" the substrates within the active site is much smaller than in the characterised members. It is not clear what effect these and other differences have on activity and specificity. Short Name:  Thymidine/pyrmidine_PPase
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2 Child Features

DB identifier Type Name
IPR018090 Family Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic
IPR013466 Family Thymidine phosphorylase/AMP phosphorylase

4 Contains

DB identifier Type Name
IPR000312 Domain Glycosyl transferase, family 3
IPR017459 Domain Glycosyl transferase family 3, N-terminal domain
IPR013102 Domain Pyrimidine nucleoside phosphorylase, C-terminal
IPR017872 Conserved_site Pyrimidine-nucleoside phosphorylase, conserved site

2 Cross Referencess

Identifier
PTHR10515
PIRSF000478

0 Found In

2 GO Annotations

GO Term Gene Name
GO:0004645 IPR000053
GO:0006206 IPR000053

2 Ontology Annotations

GO Term Gene Name
GO:0004645 IPR000053
GO:0006206 IPR000053

0 Parent Features

4 Proteins

DB identifier UniProt Accession Secondary Identifier Organism Name Length
Brdisv1pangenome1007310m.p PAC:33658400 Brachypodium distachyon Pangenome 441  
Brdisv1pangenome1007325m.p PAC:33607510 Brachypodium distachyon Pangenome 444  
Brdisv1BdTR11A1042169m.p PAC:35690474 Brachypodium distachyon BdTR11a 441  
Brdisv1BdTR11A1042188m.p PAC:35696883 Brachypodium distachyon BdTR11a 444  

3 Publications

First Author Title Year Journal Volume Pages PubMed ID
            9310231
            9698549
            9817849