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2cws

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(New page: 200px<br /><applet load="2cws" size="350" color="white" frame="true" align="right" spinBox="true" caption="2cws, resolution 1.00&Aring;" /> '''Crystal structure at...)
Current revision (13:44, 13 March 2024) (edit) (undo)
 
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[[Image:2cws.gif|left|200px]]<br /><applet load="2cws" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2cws, resolution 1.00&Aring;" />
 
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'''Crystal structure at 1.0 A of alginate lyase A1-II', a member of polysaccharide lyase family-7'''<br />
 
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==Overview==
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==Crystal structure at 1.0 A of alginate lyase A1-II', a member of polysaccharide lyase family-7==
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Alginate lyases depolymerize alginate, a heteropolysaccharide consisting, of alpha-L-guluronate and beta-D-mannuronate, through a beta-elimination, reaction. Their structure/function relationships are expected to provide, information valuable to future industrial alginate processing and drug, design for Pseudomonas aeruginosa alginate biofilm-dependent infection, but much remains unknown. Here, we present the crystal structure at 1.0 A, resolution and the results of mutational analysis of Sphingomonas sp. A1, alginate lyase A1-II', which is grouped into the polysaccharide lyase (PL), family-7. The overall structure of A1-II' uses a beta-sandwich fold, and, it has a large active cleft covered by two short flexible loops., Comparison with other family PL-7 structures indicated that loop opening, is necessary for substrate binding when the catalytic reaction is, initiated. In contrast to the disorder in many side-chains on the protein, surface, the three adjacent beta-strands at the center of the active cleft, are well ordered. This results from hydrogen bond networks and, stacking-like associations identical with those in other family PL-7, structures. Disruption of these interactions by site-directed mutagenesis, (R146A, E148A, R150A, Q189A, and K280A) makes the protein insoluble or, greatly decreases its activity. The A1-II' structure includes two sulfate, ions in the active cleft. Ammonium sulfate was a potent inhibitor with a, Ki of 2.5 mM, indicating that our structure represents a model of the, inhibitory state. Results of mutational analysis and continuous hydrogen, bond networks suggest that Arg146, Gln189, His191, and Tyr284 form an, active center. Tyr284OH appears particularly crucial to the catalytic, reaction, which is supported by sulfate ion binding and the proximity to, the C5 and O4 atoms of subsite +1 in the model obtained by energy, minimization calculations using tri-mannuronate. The structural basis, shown by this study is similar in many respects to that of the family PL-5, enzymes.
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<StructureSection load='2cws' size='340' side='right'caption='[[2cws]], [[Resolution|resolution]] 1.00&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2cws]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sphingomonas_sp._A1 Sphingomonas sp. A1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CWS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CWS FirstGlance]. <br>
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2CWS is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sphingomonas_sp._a28241 Sphingomonas sp. a28241] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Poly(beta-D-mannuronate)_lyase Poly(beta-D-mannuronate) lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.3 4.2.2.3] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CWS OCA].
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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]] 1&#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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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==Reference==
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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=2cws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2cws OCA], [https://pdbe.org/2cws PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2cws RCSB], [https://www.ebi.ac.uk/pdbsum/2cws PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2cws ProSAT]</span></td></tr>
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A structural basis for depolymerization of alginate by polysaccharide lyase family-7., Yamasaki M, Ogura K, Hashimoto W, Mikami B, Murata K, J Mol Biol. 2005 Sep 9;352(1):11-21. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16081095 16081095]
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</table>
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[[Category: Poly(beta-D-mannuronate) lyase]]
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== Function ==
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[[Category: Single protein]]
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[https://www.uniprot.org/uniprot/Q75WP3_9SPHN Q75WP3_9SPHN]
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[[Category: Sphingomonas sp. a28241]]
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== Evolutionary Conservation ==
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[[Category: Hashimoto, W.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Mikami, B.]]
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Check<jmol>
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[[Category: Murata, K.]]
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<jmolCheckbox>
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[[Category: Ogura, K.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cw/2cws_consurf.spt"</scriptWhenChecked>
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[[Category: Yamasaki, M.]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: GOL]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: SO4]]
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</jmolCheckbox>
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[[Category: alginate lyase]]
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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=2cws ConSurf].
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[[Category: polysaccharide lyase family-7]]
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<div style="clear:both"></div>
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__TOC__
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 18:50:02 2008''
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Sphingomonas sp. A1]]
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[[Category: Hashimoto W]]
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[[Category: Mikami B]]
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[[Category: Murata K]]
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[[Category: Ogura K]]
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[[Category: Yamasaki M]]

Current revision

Crystal structure at 1.0 A of alginate lyase A1-II', a member of polysaccharide lyase family-7

PDB ID 2cws

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