3kvr
From Proteopedia
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| - | + | ==Trapping of an oxocarbenium ion intermediate in UP crystals== | |
| - | + | <StructureSection load='3kvr' size='340' side='right' caption='[[3kvr]], [[Resolution|resolution]] 2.60Å' scene=''> | |
| - | + | == Structural highlights == | |
| + | <table><tr><td colspan='2'>[[3kvr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KVR FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R2G:2,5-ANHYDRO-4-DEOXY-D-ERYTHRO-PENT-4-ENITOL'>R2G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URF:5-FLUOROURACIL'>URF</scene></td></tr> | ||
| + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ku4|3ku4]], [[3kuk|3kuk]], [[3kvv|3kvv]], [[3kvy|3kvy]]</td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">UPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 Bos taurus])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </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=3kvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kvr RCSB], [http://www.ebi.ac.uk/pdbsum/3kvr PDBsum]</span></td></tr> | ||
| + | </table> | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kv/3kvr_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Uridine phosphorylase is a key enzyme in the pyrimidine salvage pathway. This enzyme catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate (or 2'-deoxyuridine to 2'-deoxyribose 1-phosphate). Here we report the structure of hexameric Escherichia coli uridine phosphorylase treated with 5-fluorouridine and sulfate and dimeric bovine uridine phosphorylase treated with 5-fluoro-2'-deoxyuridine or uridine, plus sulfate. In each case the electron density shows three separate species corresponding to the pyrimidine base, sulfate, and a ribosyl species, which can be modeled as a glycal. In the structures of the glycal complexes, the fluorouracil O2 atom is appropriately positioned to act as the base required for glycal formation via deprotonation at C2'. Crystals of bovine uridine phosphorylase treated with 2'-deoxyuridine and sulfate show intact nucleoside. NMR time course studies demonstrate that uridine phosphorylase can catalyze the hydrolysis of the fluorinated nucleosides in the absence of phosphate or sulfate, without the release of intermediates or enzyme inactivation. These results add a previously unencountered mechanistic motif to the body of information on glycal formation by enzymes catalyzing the cleavage of glycosyl bonds. | ||
| - | + | Glycal formation in crystals of uridine phosphorylase.,Paul D, O'Leary SE, Rajashankar K, Bu W, Toms A, Settembre EC, Sanders JM, Begley TP, Ealick SE Biochemistry. 2010 Apr 27;49(16):3499-509. PMID:20364833<ref>PMID:20364833</ref> | |
| - | + | ||
| - | == | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | + | </div> | |
| + | |||
| + | ==See Also== | ||
| + | *[[Uridine phosphorylase|Uridine phosphorylase]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
[[Category: Bos taurus]] | [[Category: Bos taurus]] | ||
[[Category: Uridine phosphorylase]] | [[Category: Uridine phosphorylase]] | ||
| - | [[Category: Begley, T P | + | [[Category: Begley, T P]] |
| - | [[Category: Bu, W | + | [[Category: Bu, W]] |
| - | [[Category: Ealick, S E | + | [[Category: Ealick, S E]] |
| - | [[Category: Leary, S O | + | [[Category: Leary, S O]] |
| - | [[Category: Paul, D | + | [[Category: Paul, D]] |
| - | [[Category: Rajashankar, K | + | [[Category: Rajashankar, K]] |
| - | [[Category: Sanders, J | + | [[Category: Sanders, J]] |
| - | [[Category: Settembre, E | + | [[Category: Settembre, E]] |
| - | [[Category: Toms, A | + | [[Category: Toms, A]] |
[[Category: Glycal]] | [[Category: Glycal]] | ||
[[Category: Oxocarbenium ion]] | [[Category: Oxocarbenium ion]] | ||
[[Category: Pyrimidine salvage]] | [[Category: Pyrimidine salvage]] | ||
[[Category: Transferase]] | [[Category: Transferase]] | ||
| - | [[Category: Uridine phosphorylase]] | ||
Revision as of 17:21, 18 December 2014
Trapping of an oxocarbenium ion intermediate in UP crystals
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