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| | <StructureSection load='2ewe' size='340' side='right'caption='[[2ewe]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='2ewe' size='340' side='right'caption='[[2ewe]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2ewe]] is a 1 chain structure with sequence from [https://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=2EWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EWE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2ewe]] 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=2EWE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EWE FirstGlance]. <br> |
| - | </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=ADA:ALPHA-D-GALACTOPYRANURONIC+ACID'>ADA</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"><div style='overflow: auto; max-height: 3em;'>[[1air|1air]], [[1plu|1plu]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADA:ALPHA-D-GALACTOPYRANURONIC+ACID'>ADA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pelC ([https://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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pectate_lyase Pectate lyase], with EC number [https://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=2ewe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ewe OCA], [https://pdbe.org/2ewe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ewe RCSB], [https://www.ebi.ac.uk/pdbsum/2ewe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ewe ProSAT]</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=2ewe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ewe OCA], [https://pdbe.org/2ewe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ewe RCSB], [https://www.ebi.ac.uk/pdbsum/2ewe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ewe ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://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]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Dickeya chrysanthemi]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pectate lyase]]
| + | [[Category: Jurnak F]] |
| - | [[Category: Jurnak, F]] | + | [[Category: Scavetta RD]] |
| - | [[Category: Scavetta, R D]] | + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Parallel beta helix]]
| + | |
| - | [[Category: Protein-oligosaccharide interaction]]
| + | |
| 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
The three-dimensional structure of a complex between the pectate lyase C (PelC) R218K mutant and a plant cell wall fragment has been determined by x-ray diffraction techniques to a resolution of 2.2 A and refined to a crystallographic R factor of 18.6%. The oligosaccharide substrate, alpha-D-GalpA-([1-->4]-alpha-D-GalpA)3-(1-->4)-D-GalpA , is composed of five galacturonopyranose units (D-GalpA) linked by alpha-(1-->4) glycosidic bonds. PelC is secreted by the plant pathogen Erwinia chrysanthemi and degrades the pectate component of plant cell walls in soft rot diseases. The substrate has been trapped in crystals by using the inactive R218K mutant. Four of the five saccharide units of the substrate are well ordered and represent an atomic view of the pectate component in plant cell walls. The conformation of the pectate fragment is a mix of 21 and 31 right-handed helices. The substrate binds in a cleft, interacting primarily with positively charged groups: either lysine or arginine amino acids on PelC or the four Ca2+ ions found in the complex. The observed protein-oligosaccharide interactions provide a functional explanation for many of the invariant and conserved amino acids in the pectate lyase family of proteins. Because the R218K PelC-galacturonopentaose complex represents an intermediate in the reaction pathway, the structure also reveals important details regarding the enzymatic mechanism. Notably, the results suggest that an arginine, which is invariant in the pectate lyase superfamily, is the amino acid that initiates proton abstraction during the beta elimination cleavage of polygalacturonic acid.
Structure of a plant cell wall fragment complexed to pectate lyase C.,Scavetta RD, Herron SR, Hotchkiss AT, Kita N, Keen NT, Benen JA, Kester HC, Visser J, Jurnak F Plant Cell. 1999 Jun;11(6):1081-92. PMID:10368179[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Scavetta RD, Herron SR, Hotchkiss AT, Kita N, Keen NT, Benen JA, Kester HC, Visser J, Jurnak F. Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell. 1999 Jun;11(6):1081-92. PMID:10368179
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