2d20

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[[Image:2d20.gif|left|200px]]<br /><applet load="2d20" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2d20, resolution 1.85&Aring;" />
 
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'''Crystal structure of michaelis complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86'''<br />
 
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==Overview==
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==Crystal structure of michaelis complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86==
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Xylanases hydrolyse the beta-1,4-glycosidic bonds within the xylan backbone and belong to either family 10 or 11 of the glycoside hydrolases, on the basis of the amino acid sequence similarities of their catalytic domains. Generally, xylanases have a core catalytic domain, an N and/or C-terminal substrate-binding domain and a linker region. Until now, X-ray structural analyses of family 10 xylanases have been reported only for their catalytic domains and do not contain substrate-binding domains. We have determined the crystal structure of a family 10 xylanase containing the xylan-binding domain (XBD) from Streptomyces olivaceoviridis E-86 at 1.9 A resolution. The catalytic domain comprises a (beta/alpha)(8)-barrel topologically identical to other family 10 xylanases. XBD has three similar subdomains, as suggested from a triple-repeat sequence, which are assembled against one another around a pseudo-3-fold axis, forming a galactose-binding lectin fold similar to ricin B-chain. The Gly/Pro-rich linker region connecting the catalytic domain and XBD is not visible in the electron density map, probably because of its flexibility. The interface of the two domains in the crystal is hydrophilic, where five direct hydrogen bonds and water-mediated hydrogen bonds exist. The sugar-binding residues seen in ricin/lactose complex are spatially conserved among the three subdomains in XBD, suggesting that all of the subdomains in XBD have the capacity to bind sugars. The flexible linker region enables the two domains to move independently and may provide a triple chance of substrate capturing and catalysis. The structure reported here represents an example where the metabolic enzyme uses a ricin-type lectin motif for capturing the insoluble substrate and promoting catalysis.
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<StructureSection load='2d20' size='340' side='right'caption='[[2d20]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2d20]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_olivaceoviridis Streptomyces olivaceoviridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D20 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D20 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]] 1.85&#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=NPO:P-NITROPHENOL'>NPO</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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=2d20 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d20 OCA], [https://pdbe.org/2d20 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d20 RCSB], [https://www.ebi.ac.uk/pdbsum/2d20 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d20 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/Q7SI98_STROI Q7SI98_STROI]
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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/d2/2d20_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2d20 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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Retaining glycosyl hydrolases, which catalyse both glycosylation and deglycosylation in a concerted manner, are the most abundant hydrolases. To date, their visualization has tended to be focused on glycosylation because glycosylation reactions can be visualized by inactivating deglycosylation step and/or using substrate analogues to isolate covalent intermediates. Furthermore, during structural analyses of glycosyl hydrolases with hydrolytic reaction products by the conventional soaking method, mutarotation of an anomeric carbon in the reaction products promptly and certainly occurs. This undesirable structural alteration hinders visualization of the second step in the reaction. Here, we investigated X-ray crystallographic visualization as a possible method for visualizing the conformational itinerary of a retaining xylanase from Streptomyces olivaceoviridis E-86. To clearly define the stereochemistry at the anomeric carbon during the deglycosylation step, extraneous nucleophiles, such as azide, were adopted to substitute for the missing base catalyst in an appropriate mutant. The X-ray crystallographic visualization provided snapshots of the components of the entire reaction, including the E*S complex, the covalent intermediate, breakdown of the intermediate and the enzyme-product (E*P)complex.
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==About this Structure==
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Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.,Suzuki R, Fujimoto Z, Ito S, Kawahara S, Kaneko S, Taira K, Hasegawa T, Kuno A J Biochem. 2009 Jul;146(1):61-70. Epub 2009 Mar 11. PMID:19279191<ref>PMID:19279191</ref>
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2D20 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptomyces_olivaceoviridis Streptomyces olivaceoviridis] with <scene name='pdbligand=NPO:'>NPO</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D20 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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Crystal structure of Streptomyces olivaceoviridis E-86 beta-xylanase containing xylan-binding domain., Fujimoto Z, Kuno A, Kaneko S, Yoshida S, Kobayashi H, Kusakabe I, Mizuno H, J Mol Biol. 2000 Jul 14;300(3):575-85. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10884353 10884353]
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</div>
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[[Category: Endo-1,4-beta-xylanase]]
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<div class="pdbe-citations 2d20" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Streptomyces olivaceoviridis]]
[[Category: Streptomyces olivaceoviridis]]
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[[Category: Fujimoto, Z.]]
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[[Category: Fujimoto Z]]
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[[Category: Hasegawa, T.]]
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[[Category: Hasegawa T]]
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[[Category: Ito, S.]]
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[[Category: Ito S]]
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[[Category: Kaneko, S.]]
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[[Category: Kaneko S]]
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[[Category: Kawahara, S I.]]
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[[Category: Kawahara SI]]
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[[Category: Kuno, A.]]
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[[Category: Kuno A]]
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[[Category: Suzuki, R.]]
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[[Category: Suzuki R]]
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[[Category: Taira, K.]]
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[[Category: Taira K]]
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[[Category: GOL]]
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[[Category: NPO]]
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[[Category: catalytic-site mutant]]
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[[Category: chemical rescue]]
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[[Category: michaelis complex]]
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[[Category: retaining enzyme]]
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[[Category: tim-barrel]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:54:33 2008''
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Current revision

Crystal structure of michaelis complex of catalytic-site mutant xylanase from Streptomyces olivaceoviridis E-86

PDB ID 2d20

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