2z8r

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[[Image:2z8r.gif|left|200px]]<br /><applet load="2z8r" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2z8r, resolution 1.40&Aring;" />
 
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'''Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution'''<br />
 
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==Overview==
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==Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution==
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Rhamnogalacturonan (RG) lyase produced by plant pathogenic and saprophytic microbes plays an important role in degrading plant cell walls. An extracellular RG lyase YesW from saprophytic Bacillus subtilis is a member of polysaccharide lyase family 11 and cleaves glycoside bonds in polygalacturonan as well as RG type-I through a beta-elimination reaction. Crystal structures of YesW and its complex with galacturonan disaccharide, a reaction product analogue, were determined at 1.4 and 2.5 A resolutions with final R-factors of 16.4% and 16.6%, respectively. The enzyme is composed of an eight-bladed beta-propeller with a deep cleft in the center as a basic scaffold, and its structural fold has not been seen in polysaccharide lyases analyzed thus far. Structural analysis of the disaccharide-bound YesW and a site-directed mutagenesis study suggested that Arg-452 and Lys-535 stabilize the carboxyl group of the acidic polysaccharide molecule and Tyr-595 makes a stack interaction with the sugar pyranose ring. In addition to amino acid residues binding to the disaccharide, one calcium ion, which is coordinated by Asp-401, Glu-422, His-363, and His-399, may mediate the enzyme activity. This is, to our knowledge, the first report of a new structural category with a beta-propeller fold in polysaccharide lyases and provides structural insights into substrate binding by RG lyase.
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<StructureSection load='2z8r' size='340' side='right'caption='[[2z8r]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2z8r]] 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=2Z8R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z8R FirstGlance]. <br>
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2Z8R 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 <scene name='pdbligand=CA:'>CA</scene> and <scene name='pdbligand=MPD:'>MPD</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z8R 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]] 1.4&#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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=2z8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z8r OCA], [https://pdbe.org/2z8r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z8r RCSB], [https://www.ebi.ac.uk/pdbsum/2z8r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z8r ProSAT]</span></td></tr>
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A novel structural fold in polysaccharide lyases: Bacillus subtilis family 11 rhamnogalacturonan lyase YesW with an eight-bladed beta-propeller., Ochiai A, Itoh T, Maruyama Y, Kawamata A, Mikami B, Hashimoto W, Murata K, J Biol Chem. 2007 Dec 21;282(51):37134-45. Epub 2007 Oct 17. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17947240 17947240]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/YESW_BACSU YESW_BACSU] Pectinolytic enzyme that degrades type I rhamnogalacturonan from plant cell walls and releases oligosaccharide products. Degrades rhamnogalacturonan, polygalacturonic acid, pectic acid and pectin.<ref>PMID:16682770</ref> <ref>PMID:17449691</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/z8/2z8r_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=2z8r ConSurf].
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<div style="clear:both"></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: Hashimoto, W.]]
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[[Category: Hashimoto W]]
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[[Category: Itoh, T.]]
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[[Category: Itoh T]]
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[[Category: Kawamata, A.]]
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[[Category: Kawamata A]]
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[[Category: Maruyama, Y.]]
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[[Category: Maruyama Y]]
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[[Category: Mikami, B.]]
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[[Category: Mikami B]]
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[[Category: Murata, K.]]
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[[Category: Murata K]]
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[[Category: Ochiai, A.]]
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[[Category: Ochiai A]]
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[[Category: CA]]
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[[Category: MPD]]
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[[Category: beta-propeller]]
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[[Category: lyase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:00:49 2008''
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Current revision

Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution

PDB ID 2z8r

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