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2vk7

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(New page: 200px<br /><applet load="2vk7" size="350" color="white" frame="true" align="right" spinBox="true" caption="2vk7, resolution 1.2&Aring;" /> '''THE STRUCTURE OF CLOS...)
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[[Image:2vk7.jpg|left|200px]]<br /><applet load="2vk7" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2vk7, resolution 1.2&Aring;" />
 
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'''THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES'''<br />
 
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==About this Structure==
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==THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES==
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2VK7 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Clostridium_perfringens Clostridium perfringens] with <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=FSI:'>FSI</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Known structural/functional Sites: <scene name='pdbsite=AC1:Ca Binding Site For Chain A'>AC1</scene>, <scene name='pdbsite=AC2:Fsi Binding Site For Chain A'>AC2</scene>, <scene name='pdbsite=AC3:Fsi Binding Site For Chain B'>AC3</scene>, <scene name='pdbsite=AC4:Ca Binding Site For Chain B'>AC4</scene>, <scene name='pdbsite=AC5:Ca Binding Site For Chain A'>AC5</scene> and <scene name='pdbsite=AC6:Ca Binding Site For Chain B'>AC6</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VK7 OCA].
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<StructureSection load='2vk7' size='340' side='right'caption='[[2vk7]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
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[[Category: Clostridium perfringens]]
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== Structural highlights ==
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[[Category: Exo-alpha-sialidase]]
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<table><tr><td colspan='2'>[[2vk7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_perfringens"_veillon_and_zuber_1898 "bacillus perfringens" veillon and zuber 1898]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VK7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VK7 FirstGlance]. <br>
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[[Category: Single protein]]
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FSI:5-(ACETYLAMINO)-3,5-DIDEOXY-3-FLUORO-D-ERYTHRO-ALPHA-L-MANNO-NON-2-ULOPYRANOSONIC+ACID'>FSI</scene></td></tr>
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[[Category: Chien, C.H.]]
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2bf6|2bf6]], [[2vk5|2vk5]], [[2vk6|2vk6]]</div></td></tr>
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[[Category: Newstead, S.L.]]
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] </span></td></tr>
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[[Category: Potter, J.A.]]
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vk7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vk7 OCA], [https://pdbe.org/2vk7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vk7 RCSB], [https://www.ebi.ac.uk/pdbsum/2vk7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vk7 ProSAT]</span></td></tr>
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[[Category: Taylor, G.L.]]
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</table>
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[[Category: Watts, A.G.]]
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== Evolutionary Conservation ==
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[[Category: Wilson, J.C.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Withers, S.G.]]
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Check<jmol>
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[[Category: Xu, G.]]
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<jmolCheckbox>
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[[Category: CA]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/2vk7_consurf.spt"</scriptWhenChecked>
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[[Category: FSI]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: clostridium perfringens]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: glycosidase]]
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</jmolCheckbox>
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[[Category: hydrolase]]
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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/main_output.php?pdb_ID=2vk7 ConSurf].
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[[Category: sialic acid]]
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<div style="clear:both"></div>
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[[Category: sialidase]]
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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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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 10:57:36 2008''
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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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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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<div class="pdbe-citations 2vk7" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Bacillus perfringens veillon and zuber 1898]]
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[[Category: Exo-alpha-sialidase]]
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[[Category: Large Structures]]
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[[Category: Chien, C H]]
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[[Category: Newstead, S L]]
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[[Category: Potter, J A]]
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[[Category: Taylor, G L]]
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[[Category: Watts, A G]]
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[[Category: Wilson, J C]]
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[[Category: Withers, S G]]
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[[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]]

Current revision

THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

PDB ID 2vk7

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