4xr5: Difference between revisions
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==X-ray structure of the unliganded thymidine phosphorylase from Salmonella typhimurium at 2.05 A resolution== | ==X-ray structure of the unliganded thymidine phosphorylase from Salmonella typhimurium at 2.05 A resolution== | ||
<StructureSection load='4xr5' size='340' side='right' caption='[[4xr5]], [[Resolution|resolution]] 2.05Å' scene=''> | <StructureSection load='4xr5' size='340' side='right'caption='[[4xr5]], [[Resolution|resolution]] 2.05Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4xr5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XR5 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[4xr5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XR5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XR5 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr> | ||
< | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4xr5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xr5 OCA], [https://pdbe.org/4xr5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xr5 RCSB], [https://www.ebi.ac.uk/pdbsum/4xr5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xr5 ProSAT]</span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/TYPH_SALTY TYPH_SALTY] The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis. | ||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Highly specific thymidine phosphorylases catalyze the phosphorolytic cleavage of thymidine, with the help of a phosphate ion, resulting in thymine and 2-deoxy-alpha-D-ribose 1-phosphate. Thymidine phosphorylases do not catalyze the phosphorolysis of uridine, in contrast to nonspecific pyrimidine nucleoside phosphorylases and uridine phosphorylases. Understanding the mechanism of substrate specificity on the basis of the nucleoside is essential to support rational drug-discovery investigations of new antitumour and anti-infective drugs which are metabolized by thymidine phosphorylases. For this reason, X-ray structures of the thymidine phosphorylase from Salmonella typhimurium were solved and refined: the unliganded structure at 2.05 A resolution (PDB entry 4xr5), the structure of the complex with thymidine at 2.55 A resolution (PDB entry 4yek) and that of the complex with uridine at 2.43 A resolution (PDB entry 4yyy). The various structural features of the enzyme which might be responsible for the specificity for thymidine and not for uridine were identified. The presence of the 2'-hydroxyl group in uridine results in a different position of the uridine furanose moiety compared with that of thymidine. This feature may be the key element of the substrate specificity. The specificity might also be associated with the opening/closure mechanism of the two-domain subunit structure of the enzyme. | |||
Structural investigation of the thymidine phosphorylase from Salmonella typhimurium in the unliganded state and its complexes with thymidine and uridine.,Balaev VV, Lashkov AA, Gabdulkhakov AG, Dontsova MV, Seregina TA, Mironov AS, Betzel C, Mikhailov AM Acta Crystallogr F Struct Biol Commun. 2016 Mar 1;72(Pt 3):224-33. doi:, 10.1107/S2053230X1600162X. Epub 2016 Feb 19. PMID:26919527<ref>PMID:26919527</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4xr5" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Salmonella enterica subsp. enterica serovar Typhimurium]] | ||
[[Category: | [[Category: Balaev VV]] | ||
[[Category: | [[Category: Betzel C]] | ||
[[Category: | [[Category: Gabdulkhakov AG]] | ||
[[Category: | [[Category: Lashkov AA]] | ||
[[Category: | [[Category: Mikhailov AM]] | ||