3nvd

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[[Image:3nvd.png|left|200px]]
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==Structure of YBBD in complex with pugnac==
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<StructureSection load='3nvd' size='340' side='right' caption='[[3nvd]], [[Resolution|resolution]] 1.84&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3nvd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3cqm 3cqm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NVD FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OAN:O-(2-ACETAMIDO-2-DEOXY+D-GLUCOPYRANOSYLIDENE)+AMINO-N-PHENYLCARBAMATE'>OAN</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene><br>
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<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3bmx|3bmx]]</td></tr>
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<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ybbD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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/Beta-N-acetylhexosaminidase Beta-N-acetylhexosaminidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.52 3.2.1.52] </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=3nvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nvd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nvd RCSB], [http://www.ebi.ac.uk/pdbsum/3nvd 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/nv/3nvd_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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Three-dimensional structures of NagZ of Bacillus subtilis, the first structures of a two-domain beta-N-acetylglucosaminidase of family 3 of glycosidases, were determined with and without the transition state mimicking inhibitor PUGNAc bound to the active site, at 1.84- and 1.40-A resolution, respectively. The structures together with kinetic analyses of mutants revealed an Asp-His dyad involved in catalysis: His(234) of BsNagZ acts as general acid/base catalyst and is hydrogen bonded by Asp(232) for proper function. Replacement of both His(234) and Asp(232) with glycine reduced the rate of hydrolysis of the fluorogenic substrate 4'-methylumbelliferyl N-acetyl-beta-D-glucosaminide 1900- and 4500-fold, respectively, and rendered activity pH-independent in the alkaline range consistent with a role of these residues in acid/base catalysis. N-Acetylglucosaminyl enzyme intermediate accumulated in the H234G mutant and beta-azide product was formed in the presence of sodium azide in both mutants. The Asp-His dyad is conserved within beta-N-acetylglucosaminidases but otherwise absent in beta-glycosidases of family 3, which instead carry a "classical" glutamate acid/base catalyst. The acid/base glutamate of Hordeum vulgare exoglucanase (Exo1) superimposes with His(234) of the dyad of BsNagZ and, in contrast to the latter, protrudes from a second domain of the enzyme into the active site. This is the first report of an Asp-His catalytic dyad involved in hydrolysis of glycosides resembling in function the Asp-His-Ser triad of serine proteases. Our findings will facilitate the development of mechanism-based inhibitors that selectively target family 3 beta-N-acetylglucosaminidases, which are involved in bacterial cell wall turnover, spore germination, and induction of beta-lactamase.
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<!--
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Structural and kinetic analysis of Bacillus subtilis N-acetylglucosaminidase reveals a unique Asp-His dyad mechanism.,Litzinger S, Fischer S, Polzer P, Diederichs K, Welte W, Mayer C J Biol Chem. 2010 Nov 12;285(46):35675-84. Epub 2010 Sep 7. PMID:20826810<ref>PMID:20826810</ref>
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The line below this paragraph, containing "STRUCTURE_3nvd", 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_3nvd| PDB=3nvd | SCENE= }}
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===Structure of YBBD in complex with pugnac===
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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_20826810}}, 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 20826810 is the PubMed ID number.
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</StructureSection>
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-->
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{{ABSTRACT_PUBMED_20826810}}
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==About this Structure==
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[[3nvd]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3cqm 3cqm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NVD OCA].
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==Reference==
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<ref group="xtra">PMID:020826810</ref><references group="xtra"/>
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[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: Beta-N-acetylhexosaminidase]]
[[Category: Beta-N-acetylhexosaminidase]]

Revision as of 10:31, 28 May 2014

Structure of YBBD in complex with pugnac

3nvd, resolution 1.84Å

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