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New page: left|200px<br /> <applet load="1o8f" size="450" color="white" frame="true" align="right" spinBox="true" caption="1o8f, resolution 2.20Å" /> '''PECTATE LYASE C FRO...
 
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[[Image:1o8f.gif|left|200px]]<br />
<applet load="1o8f" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1o8f, resolution 2.20&Aring;" />
'''PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 9.5 WITH 30MM CA2+'''<br />


==Overview==
==Pectate Lyase C from Erwinia Chrysanthemi at pH 9.5 with 30mM Ca2+==
Ca(2+) is essential for in vitro activity of Erwinia chrysanthemi pectate, lyase C (PelC). Crystallographic analyses of 11 PelC-Ca(2+) complexes, formed at pH 4.5, 9.5, and 11.2 under varying Ca(2+) concentrations, have, been solved and refined at a resolution of 2.2 A. The Ca(2+) site, represents a new motif for Ca(2+), consisting primarily of beta-turns and, beta-strands. The principal differences between PelC and the PelC-Ca(2+), structures at all pH values are the side-chain conformations of Asp-129, and Glu-166 as well as the occupancies of four water molecules. According, to calculations of pK(a) values, the presence of Ca(2+) and associated, structural changes lower the pK(a) of Arg-218, the amino acid responsible, for proton abstraction during catalysis. The Ca(2+) affinity for ... [[http://ispc.weizmann.ac.il/pmbin/getpm?12540845 (full description)]]
<StructureSection load='1o8f' size='340' side='right'caption='[[1o8f]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1o8f]] 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=1O8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O8F 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]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=1o8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o8f OCA], [https://pdbe.org/1o8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o8f RCSB], [https://www.ebi.ac.uk/pdbsum/1o8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o8f ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PLYC_DICCH PLYC_DICCH] Involved in maceration and soft-rotting of plant tissue.
== 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/o8/1o8f_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1o8f ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Ca(2+) is essential for in vitro activity of Erwinia chrysanthemi pectate lyase C (PelC). Crystallographic analyses of 11 PelC-Ca(2+) complexes, formed at pH 4.5, 9.5, and 11.2 under varying Ca(2+) concentrations, have been solved and refined at a resolution of 2.2 A. The Ca(2+) site represents a new motif for Ca(2+), consisting primarily of beta-turns and beta-strands. The principal differences between PelC and the PelC-Ca(2+) structures at all pH values are the side-chain conformations of Asp-129 and Glu-166 as well as the occupancies of four water molecules. According to calculations of pK(a) values, the presence of Ca(2+) and associated structural changes lower the pK(a) of Arg-218, the amino acid responsible for proton abstraction during catalysis. The Ca(2+) affinity for PelC is weak, as the K(d) was estimated to be 0.132 (+/-0.004) mm at pH 9.5, 1.09 (+/-0.29) mm at pH 11.2, and 5.84 (+/-0.41) mm at pH 4.5 from x-ray diffraction studies and 0.133 (+/-0.045) mm at pH 9.5 from intrinsic tryptophan fluorescence measurements. Given the pH dependence of Ca(2+) affinity, PelC activity at pH 4.5 has been reexamined. At saturating Ca(2+) concentrations, PelC activity increases 10-fold at pH 4.5 but is less than 1% of maximal activity at pH 9.5. Taken together, the studies suggest that the primary Ca(2+) ion in PelC has multiple functions.


==About this Structure==
Characterization and implications of Ca2+ binding to pectate lyase C.,Herron SR, Scavetta RD, Garrett M, Legner M, Jurnak F J Biol Chem. 2003 Apr 4;278(14):12271-7. Epub 2003 Jan 22. PMID:12540845<ref>PMID:12540845</ref>
1O8F 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 CA as [[http://en.wikipedia.org/wiki/ligand ligand]]. Active as [[http://en.wikipedia.org/wiki/ ]], 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=1O8F OCA]].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Characterization and implications of Ca2+ binding to pectate lyase C., Herron SR, Scavetta RD, Garrett M, Legner M, Jurnak F, J Biol Chem. 2003 Apr 4;278(14):12271-7. Epub 2003 Jan 22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12540845 12540845]
</div>
[[Category: Erwinia chrysanthemi]]
<div class="pdbe-citations 1o8f" style="background-color:#fffaf0;"></div>
[[Category: Single protein]]
== References ==
[[Category: Herron, S.R.]]
<references/>
[[Category: Jurnak, F.A.]]
__TOC__
[[Category: CA]]
</StructureSection>
[[Category: calcium binding]]
[[Category: Dickeya chrysanthemi]]
[[Category: parallel beta-helix]]
[[Category: Large Structures]]
[[Category: pectate lyase cleavage]]
[[Category: Herron SR]]
 
[[Category: Jurnak FA]]
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