|
|
| Line 3: |
Line 3: |
| | <StructureSection load='4yyy' size='340' side='right'caption='[[4yyy]], [[Resolution|resolution]] 2.43Å' scene=''> | | <StructureSection load='4yyy' size='340' side='right'caption='[[4yyy]], [[Resolution|resolution]] 2.43Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4yyy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Salty Salty]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YYY FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4yyy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium_str._LT2 Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YYY FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=URI:URIDINE'>URI</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=URI:URIDINE'>URI</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4yek|4yek]]</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=4yyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yyy OCA], [https://pdbe.org/4yyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yyy RCSB], [https://www.ebi.ac.uk/pdbsum/4yyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yyy ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">deoA, STM4568 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=99287 SALTY])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidine_phosphorylase Thymidine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.4 2.4.2.4] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4yyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yyy OCA], [http://pdbe.org/4yyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yyy RCSB], [http://www.ebi.ac.uk/pdbsum/4yyy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yyy ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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. | + | [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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 26: |
Line 23: |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Salty]] | + | [[Category: Salmonella enterica subsp. enterica serovar Typhimurium str. LT2]] |
| - | [[Category: Thymidine phosphorylase]]
| + | [[Category: Balaev VV]] |
| - | [[Category: Balaev, V V]] | + | [[Category: Betzel C]] |
| - | [[Category: Betzel, C]] | + | [[Category: Gabdulkhakov AG]] |
| - | [[Category: Gabdulkhakov, A G]] | + | [[Category: Lashkov AA]] |
| - | [[Category: Lashkov, A A]] | + | [[Category: Mikhailov AM]] |
| - | [[Category: Mikhailov, A M]] | + | |
| - | [[Category: Metabolism]]
| + | |
| - | [[Category: Nucleoside]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Balaev VV, Lashkov AA, Gabdulkhakov AG, Dontsova MV, Seregina TA, Mironov AS, Betzel C, Mikhailov AM. Structural investigation of the thymidine phosphorylase from Salmonella typhimurium in the unliganded state and its complexes with thymidine and uridine. Acta Crystallogr F Struct Biol Commun. 2016 Mar 1;72(Pt 3):224-33. doi:, 10.1107/S2053230X1600162X. Epub 2016 Feb 19. PMID:26919527 doi:http://dx.doi.org/10.1107/S2053230X1600162X
|
