2vhl

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{{Seed}}
 
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[[Image:2vhl.png|left|200px]]
 
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==The Three-dimensional structure of the N-Acetylglucosamine-6- phosphate deacetylase from Bacillus subtilis==
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The line below this paragraph, containing "STRUCTURE_2vhl", creates the "Structure Box" on the page.
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<StructureSection load='2vhl' size='340' side='right'caption='[[2vhl]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2vhl]] is a 2 chain structure with sequence from [https://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=1un7 1un7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VHL FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=GLP:GLUCOSAMINE+6-PHOSPHATE'>GLP</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></td></tr>
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{{STRUCTURE_2vhl| PDB=2vhl | SCENE= }}
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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=2vhl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vhl OCA], [https://pdbe.org/2vhl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vhl RCSB], [https://www.ebi.ac.uk/pdbsum/2vhl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vhl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NAGA_BACSU NAGA_BACSU]
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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/vh/2vhl_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=2vhl 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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The enzyme N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of GlcNAc-6-P to yield glucosamine 6-phosphate and acetate, the first committed step in the biosynthetic pathway to amino-sugar-nucleotides. It is classified into carbohydrate esterase family CE-9 (see afmb.cnrs-mrs.fr/CAZY/). Here we report the cloning, expression, and three-dimensional structure (Protein Data Bank code 1un7) determination by x-ray crystallography of the Bacillus subtilis NagA at a resolution of 2.0 A. The structure presents two domains, a (beta/alpha)(8) barrel enclosing the active center and a small beta barrel domain. The structure is dimeric, and the substrate phosphate coordination at the active center is provided by an Arg/His pair contributed from the second molecule of the dimer. Both the overall structure and the active center bear a striking similarity to the urease superfamily with two metals involved in substrate binding and catalysis. PIXE (Proton-Induced x-ray Emission) data show that iron is the predominant metal in the purified protein. We propose a catalytic mechanism involving proton donation to the leaving group by aspartate, nucleophilic attack by an Fe-bridged hydroxide, and stabilization of the carbonyl oxygen by one of the two Fe atoms of the pair. We believe that this is the first sugar deacetylase to utilize this fold and catalytic mechanism.
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===THE THREE-DIMENSIONAL STRUCTURE OF THE N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE FROM BACILLUS SUBTILIS===
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The three-dimensional structure of the N-acetylglucosamine-6-phosphate deacetylase, NagA, from Bacillus subtilis: a member of the urease superfamily.,Vincent F, Yates D, Garman E, Davies GJ, Brannigan JA J Biol Chem. 2004 Jan 23;279(4):2809-16. Epub 2003 Oct 13. PMID:14557261<ref>PMID:14557261</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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The line below this paragraph, {{ABSTRACT_PUBMED_14557261}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2vhl" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 14557261 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_14557261}}
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__TOC__
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</StructureSection>
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==About this Structure==
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2VHL is a 2 chains structure of sequences 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=1un7 1un7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VHL OCA].
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==Reference==
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<ref group="xtra">PMID:14557261</ref><references group="xtra"/>
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[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: N-acetylglucosamine-6-phosphate deacetylase]]
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[[Category: Large Structures]]
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[[Category: Davies, G J.]]
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[[Category: Davies GJ]]
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[[Category: Garman, E.]]
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[[Category: Garman E]]
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[[Category: Vincent, F.]]
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[[Category: Vincent F]]
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[[Category: Yates, D.]]
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[[Category: Yates D]]
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[[Category: Bacillus subtili]]
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[[Category: Carbohydrate metabolism]]
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[[Category: Deacetylase]]
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[[Category: Hydrolase]]
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[[Category: N- acetyleglucosamine-6-phosphate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:21:30 2009''
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Current revision

The Three-dimensional structure of the N-Acetylglucosamine-6- phosphate deacetylase from Bacillus subtilis

PDB ID 2vhl

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