1pvx: Difference between revisions

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-[[Image:1pvx.jpg|left|200px]]<br /><applet load="1pvx" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1pvx, resolution 1.59&Aring;" />
-'''DO-1,4-BETA-XYLANASE, ROOM TEMPERATURE, PH 4.5'''<br />
-==Overview==
+==DO-1,4-BETA-XYLANASE, ROOM TEMPERATURE, PH 4.5==
-A highly thermostable xylanase isolated from the thermophilic fungus, Paecilomyces varioti has been crystallized by the vapour diffusion method., The isolation of this enzyme by crystallization directly from the culture, filtrate projects this fungus as an important source for large-scale, production of pure xylanase. The crystals belong to orthorhombic space, group P2(1)2(1)2(1) with the unit cell dimensions a = 38.48 A, b = 53.87 A, and c = 90.23 A. Four molecules occupy a volume of 187,039.4 A3 along with, 34% of solvent. The data collected with an area detector to the resolution, of 2.7 A were used to calculate the unit cell parameters and Matthews', constant. The optical behaviour of the crystal was studied at different, temperatures to understand its thermal stability.
+<StructureSection load='1pvx' size='340' side='right'caption='[[1pvx]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1pvx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Paecilomyces_variotii Paecilomyces variotii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PVX 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]] 1.59&#8491;</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=1pvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pvx OCA], [https://pdbe.org/1pvx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pvx RCSB], [https://www.ebi.ac.uk/pdbsum/1pvx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pvx ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/XYNA_BYSSP XYNA_BYSSP]
+== 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/pv/1pvx_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=1pvx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We report the crystal structure at 1.59 A and the proposed amino acid sequence of an endo-1,4-beta-xylanase (PVX) from the thermophilic fungus Paecilomyces varioti Bainier (PvB), stable up to 75 degrees C. This fungus is attracting clinical attention as a pathogen causing post-surgical infections. Its xylanase, known as a skin-contact allergen, is the first protein from this fungus whose three-dimensional structure has been elucidated. The crystals of PVX conform to the space group P2(1)2(1)2(1 )with a=38.76 A, b=54.06 A and c=90.06 A. The structure was solved by molecular replacement techniques using polyalanine coordinates of the Thermomyces lanuginosus xylanase (PDB code 1YNA) and a careful model building based on the amino acid sequence known for two trypsin-digested peptide fragments (17 residues), the sequence and structural alignment of family-11 xylanases and electron density maps. The final refined model has 194 amino acid residues and 128 water molecules, with a crystallographic R-factor of 19.07 % and a free R-factor of 21.94 %. The structure belongs to an all-beta fold, with two curved beta-sheets, forming the cylindrical active-site cleft, and a lone alpha-helix, as present in other family-11 xylanases. We have carried out a quantitative comparison of the structure and sequence of the present thermophilic xylanase (PVX) with other available native structures of mesophiles and thermophiles, the first such detailed analysis to be carried out on family-11 xylanases. The analysis provides a basis for the rationalisation of the idea that the "hinge" region is made more compact in thermophiles by the addition of a disulphide bridge between Cys110 and Cys154 and a N-H.O hydrogen bond between Trp159 near the extremity of the lone alpha-helix and Trp138 on beta-strand B8. This work brings out explicitly the presence of the C-H.O and the C-H.pi type interactions in these enzymes. A complete description of structural stability of these enzymes needs to take account of these weaker interactions.
-==About this Structure==
+The tertiary structure at 1.59 A resolution and the proposed amino acid sequence of a family-11 xylanase from the thermophilic fungus Paecilomyces varioti bainier.,Kumar PR, Eswaramoorthy S, Vithayathil PJ, Viswamitra MA J Mol Biol. 2000 Jan 21;295(3):581-93. PMID:10623548<ref>PMID:10623548</ref>
-PVX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Paecilomyces_variotii Paecilomyces variotii]. 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=1PVX OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Crystallization and preliminary X-ray crystallographic studies of thermostable xylanase crystals isolated from Paecilomyces varioti., Eswaramoorthy S, Vithayathil PJ, Viswamitra MA, J Mol Biol. 1994 Nov 4;243(4):806-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7966300 7966300]
+</div>
-[[Category: Endo-1,4-beta-xylanase]]
+<div class="pdbe-citations 1pvx" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Paecilomyces variotii]]
-[[Category: Single protein]]
+[[Category: Eswaramoorthy S]]
-[[Category: Eswaramoorthy, S.]]
+[[Category: Rajeshkumar P]]
-[[Category: Rajeshkumar, P.]]
+[[Category: Viswamitra MA]]
-[[Category: Viswamitra, M.A.]]
+[[Category: Vithayathil PJ]]
-[[Category: Vithayathil, P.J.]]
-[[Category: family-11 of glycosyl hydrolases]]
-[[Category: thermophilic]]
-[[Category: xylanase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 00:10:14 2007''