1air

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(New page: 200px<br /><applet load="1air" size="450" color="white" frame="true" align="right" spinBox="true" caption="1air, resolution 2.2&Aring;" /> '''PECTATE LYASE C FROM ...)
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[[Image:1air.gif|left|200px]]<br /><applet load="1air" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1air, resolution 2.2&Aring;" />
 
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'''PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI (EC16) TO A RESOLUTION OF 2.2 ANGSTROMS WITH 128 WATERS'''<br />
 
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==Overview==
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==PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI (EC16) TO A RESOLUTION OF 2.2 ANGSTROMS WITH 128 WATERS==
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The crystal structure of pectate lyase E (PelE; EC 4.2.2.2) from the, enterobacteria Erwinia chrysanthemi has been refined by molecular dynamics, techniques to a resolution of 2.2 A and an R factor (an agreement factor, between observed structure factor amplitudes) of 16.1%. The final model, consists of all 355 amino acids and 157 water molecules. The, root-mean-square deviation from ideality is 0.009 A for bond lengths and, 1.721[deg] for bond angles. The structure of PelE bound to a lanthanum, ion, which inhibits the enzymatic activity, has also been refined and, compared to the metal-free protein. In addition, the structures of pectate, lyase C (PelC) in the presence and absence of a lutetium ion have been, refined further using an improved algorithm for identifying waters and, other solvent molecules. The two putative active site regions of PelE have, been compared to those in the refined structure of PelC. The analysis of, the atomic details of PelE and PelC in the presence and absence of, lanthanide ions provides insight into the enzymatic mechanism of pectate, lyases.
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<StructureSection load='1air' size='340' side='right'caption='[[1air]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1air]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dickeya_chrysanthemi Dickeya chrysanthemi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AIR 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]] 2.2&#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=SO4:SULFATE+ION'>SO4</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=1air FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1air OCA], [https://pdbe.org/1air PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1air RCSB], [https://www.ebi.ac.uk/pdbsum/1air PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1air ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/PLYC_DICCH PLYC_DICCH] Involved in maceration and soft-rotting of plant tissue.
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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/ai/1air_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=1air 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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The crystal structure of pectate lyase E (PelE; EC 4.2.2.2) from the enterobacteria Erwinia chrysanthemi has been refined by molecular dynamics techniques to a resolution of 2.2 A and an R factor (an agreement factor between observed structure factor amplitudes) of 16.1%. The final model consists of all 355 amino acids and 157 water molecules. The root-mean-square deviation from ideality is 0.009 A for bond lengths and 1.721[deg] for bond angles. The structure of PelE bound to a lanthanum ion, which inhibits the enzymatic activity, has also been refined and compared to the metal-free protein. In addition, the structures of pectate lyase C (PelC) in the presence and absence of a lutetium ion have been refined further using an improved algorithm for identifying waters and other solvent molecules. The two putative active site regions of PelE have been compared to those in the refined structure of PelC. The analysis of the atomic details of PelE and PelC in the presence and absence of lanthanide ions provides insight into the enzymatic mechanism of pectate lyases.
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==About this Structure==
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The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia chrysanthemi at 2.2 A Resolution.,Lietzke SE, Scavetta RD, Yoder MD, Jurnak F Plant Physiol. 1996 May;111(1):73-92. PMID:12226275<ref>PMID:12226275</ref>
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1AIR is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Erwinia_chrysanthemi Erwinia chrysanthemi] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1AIR 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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The Refined Three-Dimensional Structure of Pectate Lyase E from Erwinia chrysanthemi at 2.2 A Resolution., Lietzke SE, Scavetta RD, Yoder MD, Jurnak F, Plant Physiol. 1996 May;111(1):73-92. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12226275 12226275]
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</div>
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[[Category: Erwinia chrysanthemi]]
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<div class="pdbe-citations 1air" style="background-color:#fffaf0;"></div>
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[[Category: Pectate lyase]]
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== References ==
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[[Category: Single protein]]
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<references/>
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[[Category: Jurnak, F.A.]]
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__TOC__
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[[Category: Lietzke, S.E.]]
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</StructureSection>
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[[Category: Scavetta, R.D.]]
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[[Category: Dickeya chrysanthemi]]
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[[Category: Yoder, M.D.]]
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[[Category: Large Structures]]
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[[Category: SO4]]
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[[Category: Jurnak FA]]
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[[Category: pectate cleavage]]
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[[Category: Lietzke SE]]
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[[Category: pectinolyitc activity]]
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[[Category: Scavetta RD]]
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[[Category: trans-elimination]]
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[[Category: Yoder MD]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 10:53:17 2007''
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Current revision

PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI (EC16) TO A RESOLUTION OF 2.2 ANGSTROMS WITH 128 WATERS

PDB ID 1air

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