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| | ==Crystal Structure Analysis of Pectate Lyase PelI from Erwinia chrysanthemi== | | ==Crystal Structure Analysis of Pectate Lyase PelI from Erwinia chrysanthemi== |
| - | <StructureSection load='3b4n' size='340' side='right' caption='[[3b4n]], [[Resolution|resolution]] 1.45Å' scene=''> | + | <StructureSection load='3b4n' size='340' side='right'caption='[[3b4n]], [[Resolution|resolution]] 1.45Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3b4n]] is a 2 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=3B4N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3B4N FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3b4n]] is a 2 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=3B4N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B4N 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>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.45Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3b8y|3b8y]]</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>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pelI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=556 "Erwinia carotovora var. chrysanthemi" (Burkholder et al. 1953) Dye 1969])</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=3b4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b4n OCA], [https://pdbe.org/3b4n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b4n RCSB], [https://www.ebi.ac.uk/pdbsum/3b4n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b4n ProSAT]</span></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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3b4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b4n OCA], [http://pdbe.org/3b4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3b4n RCSB], [http://www.ebi.ac.uk/pdbsum/3b4n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3b4n ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/O50325_DICCH O50325_DICCH] Catalyzes the depolymerization of both polygalacturonate and pectins of methyl esterification degree from 22 to 89%, with an endo mode of action. In contrast to the majority of pectate lyases, displays high activity on highly methylated pectins.[RuleBase:RU367009] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b4/3b4n_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b4/3b4n_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: Castang, S]] | + | [[Category: Large Structures]] |
| - | [[Category: Creze, C]] | + | [[Category: Castang S]] |
| - | [[Category: Derivery, E]] | + | [[Category: Creze C]] |
| - | [[Category: Gouet, P]] | + | [[Category: Derivery E]] |
| - | [[Category: Haser, R]] | + | [[Category: Gouet P]] |
| - | [[Category: Shevchik, V]] | + | [[Category: Haser R]] |
| - | [[Category: Erwinia chrysanthemi]]
| + | [[Category: Shevchik V]] |
| - | [[Category: Galacturonic acid]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Pectin]]
| + | |
| - | [[Category: Right-handed parallel beta helix fold]]
| + | |
| Structural highlights
Function
O50325_DICCH Catalyzes the depolymerization of both polygalacturonate and pectins of methyl esterification degree from 22 to 89%, with an endo mode of action. In contrast to the majority of pectate lyases, displays high activity on highly methylated pectins.[RuleBase:RU367009]
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
The crystallographic structure of the family 3 polysaccharide lyase (PL-3) PelI from Erwinia chrysanthemi has been solved to 1.45 A resolution. It consists of an N-terminal domain harboring a fibronectin type III fold linked to a catalytic domain displaying a parallel beta-helix topology. The N-terminal domain is located away from the active site and is not involved in the catalytic process. After secretion in planta, the two domains are separated by E. chrysanthemi proteases. This event turns on the hypersensitive response of the host. The structure of the single catalytic domain determined to 2.1 A resolution shows that the domain separation unveils a "Velcro"-like motif of asparagines, which might be recognized by a plant receptor. The structure of PelI in complex with its substrate, a tetragalacturonate, has been solved to 2.3 A resolution. The sugar binds from subsites -2 to +2 in one monomer of the asymmetric unit, although it lies on subsites -1 to +3 in the other. These two "Michaelis complexes" have never been observed simultaneously before and are consistent with the dual mode of bond cleavage in this substrate. The bound sugar adopts a mixed 2(1) and 3(1) helical conformation similar to that reported in inactive mutants from families PL-1 and PL-10. However, our study suggests that the catalytic base in PelI is not a conventional arginine but a lysine as proposed in family PL-9.
The crystal structure of pectate lyase peli from soft rot pathogen Erwinia chrysanthemi in complex with its substrate.,Creze C, Castang S, Derivery E, Haser R, Hugouvieux-Cotte-Pattat N, Shevchik VE, Gouet P J Biol Chem. 2008 Jun 27;283(26):18260-8. Epub 2008 Apr 22. PMID:18430740[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Creze C, Castang S, Derivery E, Haser R, Hugouvieux-Cotte-Pattat N, Shevchik VE, Gouet P. The crystal structure of pectate lyase peli from soft rot pathogen Erwinia chrysanthemi in complex with its substrate. J Biol Chem. 2008 Jun 27;283(26):18260-8. Epub 2008 Apr 22. PMID:18430740 doi:http://dx.doi.org/10.1074/jbc.M709931200
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