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- Name help_outline phosphate Identifier CHEBI:43474 Charge -2 Formula HO4P InChIKeyhelp_outline NBIIXXVUZAFLBC-UHFFFAOYSA-L SMILEShelp_outline OP([O-])([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 983 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline thymidine Identifier CHEBI:17748 (Beilstein: 89285; CAS: 50-89-5) help_outline Charge 0 Formula C10H14N2O5 InChIKeyhelp_outline IQFYYKKMVGJFEH-XLPZGREQSA-N SMILEShelp_outline Cc1cn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)[nH]c1=O 2D coordinates Mol file for the small molecule Search links Involved in 10 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline 2-deoxy-α-D-ribose 1-phosphate Identifier CHEBI:57259 Charge -2 Formula C5H9O7P InChIKeyhelp_outline KBDKAJNTYKVSEK-VPENINKCSA-L SMILEShelp_outline OC[C@H]1O[C@@H](C[C@@H]1O)OP([O-])([O-])=O 2D coordinates Mol file for the small molecule Search links Involved in 8 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
- Name help_outline thymine Identifier CHEBI:17821 (Beilstein: 607626; CAS: 65-71-4) help_outline Charge 0 Formula C5H6N2O2 InChIKeyhelp_outline RWQNBRDOKXIBIV-UHFFFAOYSA-N SMILEShelp_outline Cc1c[nH]c(=O)[nH]c1=O 2D coordinates Mol file for the small molecule Search links Involved in 11 reaction(s) Find molecules that contain or resemble this structure Find proteins in UniProtKB for this molecule
Cross-references
| RHEA:16037 | RHEA:16038 | RHEA:16039 | RHEA:16040 | |
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| Reaction direction help_outline | undefined | left-to-right | right-to-left | bidirectional |
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Publications
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Molecular cloning and expression of the pyrimidine nucleoside phosphorylase gene from Bacillus stearothermophilus TH 6-2.
Okuyama K., Hamamoto T., Noguchi T., Midorikawa Y.
The pyrimidine nucleoside phosphorylase (Py-NPase) of Bacillus stearothermophilus TH 6-2 is a dimer of 46-kDa subunits and catalyzes the reversible phosphorolysis of uridine and thymidine. The gene encoding this pyrimidine nucleoside phosphorylase (pyn gene) has been cloned and sequenced from B. s ... >> More
The pyrimidine nucleoside phosphorylase (Py-NPase) of Bacillus stearothermophilus TH 6-2 is a dimer of 46-kDa subunits and catalyzes the reversible phosphorolysis of uridine and thymidine. The gene encoding this pyrimidine nucleoside phosphorylase (pyn gene) has been cloned and sequenced from B. stearothermophilus TH 6-2. The pyn gene corresponded to an open reading frame of 1299 nucleotides that translates into a putative 433 amino acid protein with a molecular weight of 46,271. The deduced amino terminal sequence of Py-NPase coincided with that previously found for the purified enzyme. The deduced amino acid sequence of Py-NPase shared significant similarity with those of human and Escherichia coli thymidine phosphorylases. The cloned pyn gene was overexpressed in E. coli cells to produce an active enzyme in large quantities that accounted for approximately 20% of the total protein. << Less
Biosci. Biotechnol. Biochem. 60:1655-1659(1996) [PubMed] [EuropePMC]
This publication is cited by 1 other entry.
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Purification and comparative properties of a pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus.
Saunders P.P., Wilson B.A., Saunders G.F.
J Biol Chem 244:3691-3697(1969) [PubMed] [EuropePMC]
This publication is cited by 2 other entries.
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The crystal structure of pyrimidine nucleoside phosphorylase in a closed conformation.
Pugmire M.J., Ealick S.E.
<h4>Background</h4>Pyrimidine nucleoside phosphorylase (PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. In lower organisms (e.g. Bacillus stearothermophilus) PYNP accepts both thymidine and uridine, whereas in mammalian and other higher org ... >> More
<h4>Background</h4>Pyrimidine nucleoside phosphorylase (PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. In lower organisms (e.g. Bacillus stearothermophilus) PYNP accepts both thymidine and uridine, whereas in mammalian and other higher organisms it is specific for thymidine (designated thymidine phosphorylase, TP). PYNP shares 40% sequence similarity (and presumably significant structural similarity) with human TP, which has been implicated as a growth factor in tumor angiogenesis. It is thought that TP undergoes a major conformational change upon substrate binding that consequently produces an active conformation.<h4>Results</h4>The crystal structure of PYNP from B. stearothermophilus with the substrate analog pseudouridine in its active site has been solved to 2.1 A resolution. This structure confirms the similarity of PYNP to TP and supports the idea of a closed active conformation, which is the result of rigid body movement of the alpha and alpha/beta domains. The active-site cleft, where the pyrimidine and phosphate substrates bind, is between the two domains. The structure reveals an asymmetric dimer in which one subunit is fully closed and the other is only partially closed.<h4>Conclusions</h4>The closed conformation of PYNP serves as a good model to better understand the domain movement and overall function of TP. Active-site residues are confirmed and a possible mechanism for substrate binding and subsequent domain movement is suggested. Potent inhibitors of TP might have significant therapeutic value in various chemotherapeutic strategies, and the structure of PYNP should provide valuable insight into the rational design of such inhibitors. << Less
Structure 6:1467-1479(1998) [PubMed] [EuropePMC]
This publication is cited by 1 other entry.
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Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli.
Sevin D.C., Fuhrer T., Zamboni N., Sauer U.
Our understanding of metabolism is limited by a lack of knowledge about the functions of many enzymes. Here, we develop a high-throughput mass spectrometry approach to comprehensively profile proteins for in vitro enzymatic activity. Overexpressed or purified proteins are incubated in a supplement ... >> More
Our understanding of metabolism is limited by a lack of knowledge about the functions of many enzymes. Here, we develop a high-throughput mass spectrometry approach to comprehensively profile proteins for in vitro enzymatic activity. Overexpressed or purified proteins are incubated in a supplemented metabolome extract containing hundreds of biologically relevant candidate substrates, and accumulating and depleting metabolites are determined by nontargeted mass spectrometry. By combining chemometrics and database approaches, we established an automated pipeline for unbiased annotation of the functions of novel enzymes. In screening all 1,275 functionally uncharacterized Escherichia coli proteins, we discovered 241 potential novel enzymes, 12 of which we experimentally validated. Our high-throughput in vitro metabolomics method is generally applicable to any purified protein or crude cell lysate of its overexpression host and enables performing up to 1,200 nontargeted enzyme assays per working day. << Less
Nat. Methods 14:187-194(2017) [PubMed] [EuropePMC]
This publication is cited by 30 other entries.
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Purification and characterization of purine nucleoside phosphorylase and pyrimidine nucleoside phosphorylase from Bacillus stearothermophilus TH 6-2.
Hamamoto T., Noguchi T., Midorikawa Y.
The purine nucleoside phosphorylase (Pu-NPase) and the pyrimidine nucleoside phosphorylase (Py-NPase) have been purified from Bacillus stearothermophilus TH 6-2. The Pu-NPase is a trimer of 30-kDa subunits and the Py-NPase is a dimer of 46-kDa subunits. The isoelectric points of Pu-NPase and Py-NP ... >> More
The purine nucleoside phosphorylase (Pu-NPase) and the pyrimidine nucleoside phosphorylase (Py-NPase) have been purified from Bacillus stearothermophilus TH 6-2. The Pu-NPase is a trimer of 30-kDa subunits and the Py-NPase is a dimer of 46-kDa subunits. The isoelectric points of Pu-NPase and Py-NPase were pH 4.3 and 4.6, respectively. The Pu-NPase could catalyze the phosphorolysis of inosine and guanosine, but not adenosine. the Py-NPase could phosphorolyze both uridine and thymidine. << Less
Biosci. Biotechnol. Biochem. 60:1179-1180(1996) [PubMed] [EuropePMC]
This publication is cited by 2 other entries.