2xce

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[[Image:2xce.png|left|200px]]
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==Structure of YncF in complex with dUpNHpp==
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<StructureSection load='2xce' size='340' side='right' caption='[[2xce]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2xce]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XCE OCA]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xcd|2xcd]]</td></tr>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2xce FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xce OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xce RCSB], [http://www.ebi.ac.uk/pdbsum/2xce PDBsum]</span></td></tr>
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<table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/xc/2xce_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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dUTPases are a ubiquitous family of enzymes that are essential for all organisms and catalyse the breakdown of 2-deoxyuridine triphosphate (dUTP). In Bacillus subtilis there are two homotrimeric dUTPases: a genomic and a prophage form. Here, the structures of the genomic dUTPase and of its complex with the substrate analogue dUpNHpp and calcium are described, both at 1.85 A resolution. The overall fold resembles that of previously solved trimeric dUTPases. The C-terminus, which contains one of the conserved sequence motifs, is disordered in both structures. The crystal of the complex contains six independent protomers which accommodate six dUpNHpp molecules, with three triphosphates in the trans conformation and the other three in the active gauche conformation. The structure of the complex confirms the role of several key residues that are involved in ligand binding and the position of the catalytic water. Asp82, which has previously been proposed to act as a general base, points away from the active site. In the complex Ser64 reorients in order to hydrogen bond the phosphate chain of the substrate. A novel feature has been identified: the position in the sequence of the ;Phe-lid', which packs against the uracil moiety, is adjacent to motif III, whereas in all other dUTPase structures the lid is in a conserved position in motif V of the flexible C-terminal arm. This requires a reconsideration of some aspects of the accepted mechanism.
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The structure of the genomic Bacillus subtilis dUTPase: novel features in the Phe-lid.,Garcia-Nafria J, Burchell L, Takezawa M, Rzechorzek NJ, Fogg MJ, Wilson KS Acta Crystallogr D Biol Crystallogr. 2010 Sep;66(Pt 9):953-61. Epub 2010 Aug 13. PMID:20823546<ref>PMID:20823546</ref>
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The line below this paragraph, containing "STRUCTURE_2xce", creates the "Structure Box" on the page.
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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or leave the SCENE parameter empty for the default display.
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-->
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{{STRUCTURE_2xce| PDB=2xce | SCENE= }}
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===Structure of YncF in complex with dUpNHpp===
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<!--
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<references/>
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The line below this paragraph, {{ABSTRACT_PUBMED_20823546}}, adds the Publication Abstract to the page
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__TOC__
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(as it appears on PubMed at http://www.pubmed.gov), where 20823546 is the PubMed ID number.
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</StructureSection>
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-->
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{{ABSTRACT_PUBMED_20823546}}
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==About this Structure==
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[[2xce]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XCE OCA].
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==Reference==
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<ref group="xtra">PMID:020823546</ref><references group="xtra"/>
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[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: DUTP diphosphatase]]
[[Category: DUTP diphosphatase]]

Revision as of 07:44, 14 May 2014

Structure of YncF in complex with dUpNHpp

2xce, resolution 1.85Å

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