1vbr: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

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-[[Image:1vbr.gif|left|200px]]<br /><applet load="1vbr" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1vbr, resolution 1.80&Aring;" />
-'''Crystal structure of complex xylanase 10B from Thermotoga maritima with xylobiose'''<br />
-==Overview==
+==Crystal structure of complex xylanase 10B from Thermotoga maritima with xylobiose==
-The crystal structure of xylanase 10B from Thermotoga maritima MSB8, (TmxB), a hyperthermostable xylanase, has been solved in its native form, and in complex with xylobiose or xylotriose at 1.8 A resolution. In order, to gain insight into the substrate subsite and the molecular features for, thermal stability, we compared TmxB with family 10 xylanase structures, from nine microorganisms. As expected, TmxB folds into a, (beta/alpha)8-barrel structure, which is common among the glycoside, hydrolase family 10. The enzyme active site and the environment, surrounding the xylooligosaccharide of TmxB are highly similar to those of, family 10 xylanases. However, only two xylose moieties were found in its, binding pocket from the TmxB-xylotriose complex structure. This finding, suggests that TmxB could be a potential biocatalyst for the large-scale, production of xylobiose. The result of structural analyses also indicated, that TmxB possesses some additional features that account for its, thermostability. In particular, clusters of aromatic residues together, with a lack of exposed hydrophobic residues are characteristic of the TmxB, structure. TmxB has also a significant number of ion pairs on the protein, surface that are not found in other thermophilic family 10 xylanases.
+<StructureSection load='1vbr' size='340' side='right'caption='[[1vbr]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1vbr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VBR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VBR FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</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=1vbr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vbr OCA], [https://pdbe.org/1vbr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vbr RCSB], [https://www.ebi.ac.uk/pdbsum/1vbr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vbr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9WXS5_THEMA Q9WXS5_THEMA]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vb/1vbr_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1vbr ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a hyperthermostable xylanase, has been solved in its native form and in complex with xylobiose or xylotriose at 1.8 A resolution. In order to gain insight into the substrate subsite and the molecular features for thermal stability, we compared TmxB with family 10 xylanase structures from nine microorganisms. As expected, TmxB folds into a (beta/alpha)8-barrel structure, which is common among the glycoside hydrolase family 10. The enzyme active site and the environment surrounding the xylooligosaccharide of TmxB are highly similar to those of family 10 xylanases. However, only two xylose moieties were found in its binding pocket from the TmxB-xylotriose complex structure. This finding suggests that TmxB could be a potential biocatalyst for the large-scale production of xylobiose. The result of structural analyses also indicated that TmxB possesses some additional features that account for its thermostability. In particular, clusters of aromatic residues together with a lack of exposed hydrophobic residues are characteristic of the TmxB structure. TmxB has also a significant number of ion pairs on the protein surface that are not found in other thermophilic family 10 xylanases.
-==About this Structure==
+Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.,Ihsanawati, Kumasaka T, Kaneko T, Morokuma C, Yatsunami R, Sato T, Nakamura S, Tanaka N Proteins. 2005 Dec 1;61(4):999-1009. PMID:16247799<ref>PMID:16247799</ref>
-VBR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with ACY as [http://en.wikipedia.org/wiki/ligand ligand]. 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VBR OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8., Ihsanawati, Kumasaka T, Kaneko T, Morokuma C, Yatsunami R, Sato T, Nakamura S, Tanaka N, Proteins. 2005 Dec 1;61(4):999-1009. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16247799 16247799]
+</div>
-[[Category: Endo-1,4-beta-xylanase]]
+<div class="pdbe-citations 1vbr" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermotoga maritima]]
 [[Category: Ihsanawati]]
-[[Category: Kaneko, T.]]
+[[Category: Kaneko T]]
-[[Category: Kumasaka, T.]]
+[[Category: Kumasaka T]]
-[[Category: Nakamura, S.]]
+[[Category: Nakamura S]]
-[[Category: Tanaka, N.]]
+[[Category: Tanaka N]]
-[[Category: ACY]]
-[[Category: xylanase 10b]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:03:42 2007''