1w1a

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[[Image:1w1a.gif|left|200px]]<br />
 
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<applet load="1w1a" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1w1a, resolution 2.25&Aring;" />
 
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'''STRUCTURE OF BACILLUS SUBTILIS PDAA IN COMPLEX WITH NAG, A FAMILY 4 CARBOHYDRATE ESTERASE.'''<br />
 
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==Overview==
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==Structure of Bacillus subtilis PdaA in complex with NAG, a family 4 Carbohydrate esterase.==
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Family 4 carbohydrate esterases deacetylate polymeric carbohydrate, substrates such as chitin, acetyl xylan and peptidoglycan. Although some, of these enzymes have recently been enzymologically characterised, neither, their structure nor their reaction mechanism has been defined. Sequence, conservation in this family has pointed to a conserved core, termed the, NodB homology domain. We describe the cloning, purification and 1.9 A, crystal structure of PdaA, a peptidoglycan deacetylase from Bacillus, subtilis. The enzyme assumes a fold related to a (beta/alpha)8 barrel, with a long groove on the surface of the protein that harbours all, conserved residues. A complex with the substrate analogue, N-acetyl-glucosamine was refined to 2.25 A resolution, revealing, interactions of an aspartic ... [[http://ispc.weizmann.ac.il/pmbin/getpm?15251431 (full description)]]
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<StructureSection load='1w1a' size='340' side='right'caption='[[1w1a]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1w1a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W1A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W1A FirstGlance]. <br>
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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]] 2.25&#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=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></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=1w1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w1a OCA], [https://pdbe.org/1w1a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w1a RCSB], [https://www.ebi.ac.uk/pdbsum/1w1a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w1a ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PDAA_BACSU PDAA_BACSU] Catalyzes the deacetylation of N-acetylmuramic acid (MurNAc) residues in glycan strands of peptidoglycan, leading to the formation of muramic delta-lactam residues in spore cortex, after transpeptidation of deacetylated muramic acid residues. PdaA probably carries out both deacetylation and lactam ring formation and requires the product of CwlD activity on peptidoglycan as a substrate. Is required for germination. Cannot use chitin oligomer (hexa-N-acetylchitohexaose) as a substrate.<ref>PMID:12374835</ref> <ref>PMID:14679227</ref> <ref>PMID:15687192</ref>
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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/w1/1w1a_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=1w1a 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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Family 4 carbohydrate esterases deacetylate polymeric carbohydrate substrates such as chitin, acetyl xylan and peptidoglycan. Although some of these enzymes have recently been enzymologically characterised, neither their structure nor their reaction mechanism has been defined. Sequence conservation in this family has pointed to a conserved core, termed the NodB homology domain. We describe the cloning, purification and 1.9 A crystal structure of PdaA, a peptidoglycan deacetylase from Bacillus subtilis. The enzyme assumes a fold related to a (beta/alpha)8 barrel, with a long groove on the surface of the protein that harbours all conserved residues. A complex with the substrate analogue N-acetyl-glucosamine was refined to 2.25 A resolution, revealing interactions of an aspartic acid and three histidines, all conserved in the NodB homology domain, with the ligand. The PdaA structure provides a template for interpreting the wealth of sequence data on family 4 carbohydrate esterases in a structural context and represents a first step towards understanding the reaction mechanism of this family of enzymes.
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==About this Structure==
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Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N-acetyl-glucosamine.,Blair DE, van Aalten DM FEBS Lett. 2004 Jul 16;570(1-3):13-9. PMID:15251431<ref>PMID:15251431</ref>
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1W1A is a [[http://en.wikipedia.org/wiki/Single_protein Single protein]] structure of sequence from [[http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]] with NDG, CD and GOL as [[http://en.wikipedia.org/wiki/ligands ligands]]. Structure known Active Site: 1. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1W1A OCA]].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Structures of Bacillus subtilis PdaA, a family 4 carbohydrate esterase, and a complex with N-acetyl-glucosamine., Blair DE, van Aalten DM, FEBS Lett. 2004 Jul 16;570(1-3):13-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15251431 15251431]
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</div>
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<div class="pdbe-citations 1w1a" 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>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Aalten, D.M.F.Van.]]
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[[Category: Blair DE]]
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[[Category: Blair, D.E.]]
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[[Category: Van Aalten DMF]]
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[[Category: CD]]
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[[Category: GOL]]
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[[Category: NDG]]
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[[Category: deacetylase]]
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[[Category: family 4 carbohydrate esterase]]
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[[Category: hydrolase]]
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[[Category: nodb homology domain]]
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[[Category: peptidoglycan]]
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[[Category: sporulation]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 16:21:33 2007''
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Current revision

Structure of Bacillus subtilis PdaA in complex with NAG, a family 4 Carbohydrate esterase.

PDB ID 1w1a

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