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2qx3

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[[Image:2qx3.jpg|left|200px]]
 
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{{Structure
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==Structure of pectate lyase II from Xanthomonas campestris pv. campestris str. ATCC 33913==
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|PDB= 2qx3 |SIZE=350|CAPTION= <scene name='initialview01'>2qx3</scene>, resolution 2.000&Aring;
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<StructureSection load='2qx3' size='340' side='right'caption='[[2qx3]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Po4+Binding+Site+For+Residue+B+1'>AC1</scene>, <scene name='pdbsite=AC2:Po4+Binding+Site+For+Residue+A+2'>AC2</scene>, <scene name='pdbsite=AC3:Po4+Binding+Site+For+Residue+B+3'>AC3</scene>, <scene name='pdbsite=AC4:Po4+Binding+Site+For+Residue+A+4'>AC4</scene> and <scene name='pdbsite=AC5:Po4+Binding+Site+For+Residue+B+5'>AC5</scene>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=PO4:PHOSPHATE ION'>PO4</scene>
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<table><tr><td colspan='2'>[[2qx3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris Xanthomonas campestris pv. campestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QX3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QX3 FirstGlance]. <br>
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|ACTIVITY= [http://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.2 4.2.2.2]
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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]] 2&#8491;</td></tr>
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|GENE= pelB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=340 Xanthomonas campestris pv. campestris])
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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}}
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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=2qx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qx3 OCA], [https://pdbe.org/2qx3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qx3 RCSB], [https://www.ebi.ac.uk/pdbsum/2qx3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qx3 ProSAT]</span></td></tr>
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</table>
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'''Structure of pectate lyase II from Xanthomonas campestris pv. campestris str. ATCC 33913'''
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== Function ==
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[https://www.uniprot.org/uniprot/Q8P6Z9_XANCP Q8P6Z9_XANCP]
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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In the vast number of random mutagenesis experiments that have targeted protein thermostability, single amino acid substitutions that increase the apparent melting temperature (Tm) of the enzyme more than 1 to 2 degrees C are rare and often require the creation of a large library of mutated genes. Here we present a case where a single beneficial mutation (R236F) of a hemp fiber-processing pectate lyase of Xanthomonas campestris origin (PL(Xc)) produced a 6 degrees C increase in Tm and a 23-fold increase in the half-life at 45 degrees C without compromising the enzyme's catalytic efficiency. This success was based on a variation of sequence alignment strategy where a mesophilic amino acid sequence is matched with the sequences of its thermophilic counterparts that have established Tm values. Altogether, two-thirds of the nine targeted single amino acid substitutions were found to have effects either on the thermostability or on the catalytic activity of the enzyme, evidence of a high success rate of mutation without the creation of a large gene library and subsequent screening of clones. Combination of R236F with another beneficial mutation (A31G) resulted in at least a twofold increase in specific activity while preserving the improved Tm value. To understand the structural basis for the increased thermal stability or activity, the variant R236F and A31G R236F proteins and wild-type PL(Xc) were purified and crystallized. By structure analysis and computational methods, hydrophobic desolvation was found to be the driving force for the increased stability with R236F.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qx/2qx3_consurf.spt"</scriptWhenChecked>
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2QX3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris Xanthomonas campestris pv. campestris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QX3 OCA].
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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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==Reference==
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</jmolCheckbox>
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Improvement of the thermostability and activity of a pectate lyase by single amino acid substitutions, using a strategy based on melting-temperature-guided sequence alignment., Xiao Z, Bergeron H, Grosse S, Beauchemin M, Garron ML, Shaya D, Sulea T, Cygler M, Lau PC, Appl Environ Microbiol. 2008 Feb;74(4):1183-9. Epub 2007 Dec 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18156340 18156340]
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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=2qx3 ConSurf].
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[[Category: Pectate lyase]]
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<div style="clear:both"></div>
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[[Category: Single protein]]
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Xanthomonas campestris pv. campestris]]
[[Category: Xanthomonas campestris pv. campestris]]
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[[Category: Garron, M L.]]
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[[Category: Garron ML]]
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[[Category: Shaya, D.]]
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[[Category: Shaya D]]
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[[Category: PO4]]
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[[Category: lyase]]
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[[Category: parallel beta helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:30:34 2008''
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Current revision

Structure of pectate lyase II from Xanthomonas campestris pv. campestris str. ATCC 33913

PDB ID 2qx3

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