2vk5

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[[Image:2vk5.png|left|200px]]
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==THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES==
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<StructureSection load='2vk5' size='340' side='right' caption='[[2vk5]], [[Resolution|resolution]] 0.97&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2vk5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VK5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VK5 FirstGlance]. <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=GOL:GLYCEROL'>GOL</scene><br>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2bf6|2bf6]], [[2vk7|2vk7]], [[2vk6|2vk6]]</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/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </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=2vk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vk5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vk5 RCSB], [http://www.ebi.ac.uk/pdbsum/2vk5 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/vk/2vk5_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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Clostridium perfringens is a Gram-positive bacterium responsible for bacteremia, gas gangrene, and occasionally food poisoning. Its genome encodes three sialidases, nanH, nanI, and nanJ, that are involved in the removal of sialic acids from a variety of glycoconjugates and that play a role in bacterial nutrition and pathogenesis. Recent studies on trypanosomal (trans-) sialidases have suggested that catalysis in all sialidases may proceed via a covalent intermediate similar to that of other retaining glycosidases. Here we provide further evidence to support this suggestion by reporting the 0.97A resolution atomic structure of the catalytic domain of the C. perfringens NanI sialidase, and complexes with its substrate sialic acid (N-acetylneuramic acid) also to 0.97A resolution, with a transition-state analogue (2-deoxy-2,3-dehydro-N-acetylneuraminic acid) to 1.5A resolution, and with a covalent intermediate formed using a fluorinated sialic acid analogue to 1.2A resolution. Together, these structures provide high resolution snapshots along the catalytic pathway. The crystal structures suggested that NanI is able to hydrate 2-deoxy-2,3-dehydro-N-acetylneuraminic acid to N-acetylneuramic acid. This was confirmed by NMR, and a mechanism for this activity is suggested.
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<!--
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The structure of Clostridium perfringens NanI sialidase and its catalytic intermediates.,Newstead SL, Potter JA, Wilson JC, Xu G, Chien CH, Watts AG, Withers SG, Taylor GL J Biol Chem. 2008 Apr 4;283(14):9080-8. Epub 2008 Jan 24. PMID:18218621<ref>PMID:18218621</ref>
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The line below this paragraph, containing "STRUCTURE_2vk5", 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_2vk5| PDB=2vk5 | SCENE= }}
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===THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES===
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From MEDLINE&reg;/PubMed&reg;, 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_18218621}}, 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 18218621 is the PubMed ID number.
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</StructureSection>
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-->
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{{ABSTRACT_PUBMED_18218621}}
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==About this Structure==
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[[2vk5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VK5 OCA].
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==Reference==
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<ref group="xtra">PMID:18218621</ref><references group="xtra"/>
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[[Category: Clostridium perfringens]]
[[Category: Clostridium perfringens]]
[[Category: Exo-alpha-sialidase]]
[[Category: Exo-alpha-sialidase]]
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[[Category: Withers, S G.]]
[[Category: Withers, S G.]]
[[Category: Xu, G.]]
[[Category: Xu, G.]]
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[[Category: Clostridium perfringen]]
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[[Category: Glycosidase]]
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[[Category: Hydrolase]]
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[[Category: Sialic acid]]
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[[Category: Sialidase]]

Revision as of 01:12, 1 October 2014

THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

2vk5, resolution 0.97Å

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