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2vk7

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[[Image:2vk7.jpg|left|200px]]
 
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{{Structure
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==THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES==
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|PDB= 2vk7 |SIZE=350|CAPTION= <scene name='initialview01'>2vk7</scene>, resolution 1.2&Aring;
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<StructureSection load='2vk7' size='340' side='right'caption='[[2vk7]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
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|SITE= <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>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=FSI:5-(ACETYLAMINO)-2,6-ANHYDRO-3,5-DIDEOXY-3-FLUORONONONIC ACID'>FSI</scene>
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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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|ACTIVITY= [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]
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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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|GENE=
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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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}}
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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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<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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</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/2vk7_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/main_output.php?pdb_ID=2vk7 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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'''THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES'''
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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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==About this Structure==
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</div>
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2VK7 is a [[Single protein]] structure of 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=2VK7 OCA].
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<div class="pdbe-citations 2vk7" style="background-color:#fffaf0;"></div>
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[[Category: Clostridium perfringens]]
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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]]
[[Category: Exo-alpha-sialidase]]
[[Category: Exo-alpha-sialidase]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Chien, C H.]]
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[[Category: Chien, C H]]
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[[Category: Newstead, S L.]]
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[[Category: Newstead, S L]]
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[[Category: Potter, J A.]]
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[[Category: Potter, J A]]
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[[Category: Taylor, G L.]]
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[[Category: Taylor, G L]]
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[[Category: Watts, A G.]]
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[[Category: Watts, A G]]
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[[Category: Wilson, J C.]]
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[[Category: Wilson, J C]]
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[[Category: Withers, S G.]]
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[[Category: Withers, S G]]
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[[Category: Xu, G.]]
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[[Category: Xu, G]]
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[[Category: CA]]
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[[Category: Clostridium perfringen]]
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[[Category: FSI]]
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[[Category: Glycosidase]]
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[[Category: clostridium perfringen]]
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[[Category: Hydrolase]]
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[[Category: glycosidase]]
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[[Category: Sialic acid]]
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[[Category: hydrolase]]
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[[Category: Sialidase]]
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[[Category: sialic acid]]
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[[Category: sialidase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:47:22 2008''
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Current revision

THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

PDB ID 2vk7

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