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| - | ==PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI AT PH 9.5 WITH 0.3mM CA2+ added== | + | ==Pectate Lyase C from Erwinia Chrysanthemi at pH 9.5 with 0.3mM Ca2+ Added== |
| - | <StructureSection load='1o8h' size='340' side='right' caption='[[1o8h]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='1o8h' size='340' side='right'caption='[[1o8h]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1o8h]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"erwinia_carotovora_var._chrysanthemi"_(burkholder_et_al._1953)_dye_1969 "erwinia carotovora var. chrysanthemi" (burkholder et al. 1953) dye 1969]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1O8H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1O8H FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1o8h]] 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=1O8H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1O8H FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1air|1air]], [[1o88|1o88]], [[1o8d|1o8d]], [[1o8e|1o8e]], [[1o8f|1o8f]], [[1o8g|1o8g]], [[1o8i|1o8i]], [[1o8j|1o8j]], [[1o8k|1o8k]], [[1o8l|1o8l]], [[1o8m|1o8m]], [[1plu|1plu]], [[2pec|2pec]]</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></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=1o8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o8h OCA], [https://pdbe.org/1o8h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1o8h RCSB], [https://www.ebi.ac.uk/pdbsum/1o8h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1o8h ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1o8h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1o8h OCA], [http://pdbe.org/1o8h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1o8h RCSB], [http://www.ebi.ac.uk/pdbsum/1o8h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1o8h ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PLYC_DICCH PLYC_DICCH]] Involved in maceration and soft-rotting of plant tissue. | + | [https://www.uniprot.org/uniprot/PLYC_DICCH PLYC_DICCH] Involved in maceration and soft-rotting of plant tissue. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o8/1o8h_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/o8/1o8h_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pectate lyase]] | + | [[Category: Dickeya chrysanthemi]] |
| - | [[Category: Herron, S R]] | + | [[Category: Large Structures]] |
| - | [[Category: Jurnak, F A]] | + | [[Category: Herron SR]] |
| - | [[Category: Calcium binding]] | + | [[Category: Jurnak FA]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Parallel beta- helix]]
| + | |
| - | [[Category: Pectate lyase cleavage]]
| + | |
| Structural highlights
Function
PLYC_DICCH Involved in maceration and soft-rotting of plant tissue.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Herron SR, Scavetta RD, Garrett M, Legner M, Jurnak F. Characterization and implications of Ca2+ binding to pectate lyase C. J Biol Chem. 2003 Apr 4;278(14):12271-7. Epub 2003 Jan 22. PMID:12540845 doi:http://dx.doi.org/10.1074/jbc.M209306200
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