2z8r: Difference between revisions

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[[Image:2z8r.gif|left|200px]]


{{Structure
==Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution==
|PDB= 2z8r |SIZE=350|CAPTION= <scene name='initialview01'>2z8r</scene>, resolution 1.40&Aring;
<StructureSection load='2z8r' size='340' side='right'caption='[[2z8r]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> and <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>
<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>
|ACTIVITY=  
</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>
|GENE= yesW ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])
<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>
}}
<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>
 
</table>
'''Crystal structure of rhamnogalacturonan lyase YesW at 1.40 A resolution'''
== Function ==
 
[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>
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
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.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z8/2z8r_consurf.spt"</scriptWhenChecked>
2Z8R is a [[Single protein]] structure of sequence from [http://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].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
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://www.ncbi.nlm.nih.gov/pubmed/17947240 17947240]
</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].
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Hashimoto, W.]]
[[Category: Hashimoto W]]
[[Category: Itoh, T.]]
[[Category: Itoh T]]
[[Category: Kawamata, A.]]
[[Category: Kawamata A]]
[[Category: Maruyama, Y.]]
[[Category: Maruyama Y]]
[[Category: Mikami, B.]]
[[Category: Mikami B]]
[[Category: Murata, K.]]
[[Category: Murata K]]
[[Category: Ochiai, A.]]
[[Category: Ochiai A]]
[[Category: CA]]
[[Category: MPD]]
[[Category: beta-propeller]]
[[Category: lyase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:52:56 2008''
Retrieved from "https://proteopedia.org/2z8r"