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| | ==Crystal structure of pectate lyase Pel9A== | | ==Crystal structure of pectate lyase Pel9A== |
| - | <StructureSection load='1ru4' size='340' side='right' caption='[[1ru4]], [[Resolution|resolution]] 1.60Å' scene=''> | + | <StructureSection load='1ru4' size='340' side='right'caption='[[1ru4]], [[Resolution|resolution]] 1.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1ru4]] 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=1RU4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RU4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1ru4]] 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=1RU4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RU4 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]] 1.6Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PelL ([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='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=1ru4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ru4 OCA], [https://pdbe.org/1ru4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ru4 RCSB], [https://www.ebi.ac.uk/pdbsum/1ru4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ru4 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=1ru4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ru4 OCA], [http://pdbe.org/1ru4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ru4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ru4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ru4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/PLYL_DICCH PLYL_DICCH]] Presents an endo-cleaving activity on polygalacturonate or partially methylated pectin. | + | [https://www.uniprot.org/uniprot/PLYL_DICD3 PLYL_DICD3] Presents an endo-cleaving activity on polygalacturonate or partially methylated pectin. Is effective in the maceration of plant tissue, and has an important role in soft-rot disease. Is 280-fold less active against polygalacturonate than the major pectate lyase PelB. When assayed on polygalacturonate, PelL releases oligogalacturonates of different sizes; upon prolonged incubation, PelL degrades the primary products to unsaturated tetramer and pentamer in addition to unsaturated dimer and trimer. When assayed on oligogalacturonates (degrees of polymerization of 2 to 8), it preferentially forms unsaturated tetramer, and displays the highest activity on the octamer.<ref>PMID:10368144</ref> <ref>PMID:8577252</ref> |
| | == 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/ru/1ru4_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ru/1ru4_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: Hugouvieux-Cotte-Pattat, N]] | + | [[Category: Large Structures]] |
| - | [[Category: Jenkins, J]] | + | [[Category: Hugouvieux-Cotte-Pattat N]] |
| - | [[Category: Pickersgill, R W]] | + | [[Category: Jenkins J]] |
| - | [[Category: Shevchik, V E]] | + | [[Category: Pickersgill RW]] |
| - | [[Category: Lyase]]
| + | [[Category: Shevchik VE]] |
| - | [[Category: Parallel beta-helix]]
| + | |
| Structural highlights
Function
PLYL_DICD3 Presents an endo-cleaving activity on polygalacturonate or partially methylated pectin. Is effective in the maceration of plant tissue, and has an important role in soft-rot disease. Is 280-fold less active against polygalacturonate than the major pectate lyase PelB. When assayed on polygalacturonate, PelL releases oligogalacturonates of different sizes; upon prolonged incubation, PelL degrades the primary products to unsaturated tetramer and pentamer in addition to unsaturated dimer and trimer. When assayed on oligogalacturonates (degrees of polymerization of 2 to 8), it preferentially forms unsaturated tetramer, and displays the highest activity on the octamer.[1] [2]
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 "family 9 polysaccharide lyase" pectate lyase L (Pel9A) from Erwinia chrysanthemi comprises a 10-coil parallel beta-helix domain with distinct structural features including an asparagine ladder and aromatic stack at novel positions within the superhelical structure. Pel9A has a single high affinity calcium-binding site strikingly similar to the "primary" calcium-binding site described previously for the family Pel1A pectate lyases, and there is strong evidence for a common second calcium ion that binds between enzyme and substrate in the "Michaelis" complex. Although the primary calcium ion binds substrate in subsite -1, it is the second calcium ion, whose binding site is formed by the coming together of enzyme and substrate, that facilitates abstraction of the C5 proton from the sacharride in subsite +1. The role of the second calcium is to withdraw electrons from the C6 carboxylate of the substrate, thereby acidifying the C5 proton facilitating its abstraction and resulting in an E1cb-like anti-beta-elimination mechanism. The active site geometries and mechanism of Pel1A and Pel9A are closely similar, but the catalytic base is a lysine in the Pel9A enzymes as opposed to an arginine in the Pel1A enzymes.
The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi.,Jenkins J, Shevchik VE, Hugouvieux-Cotte-Pattat N, Pickersgill RW J Biol Chem. 2004 Mar 5;279(10):9139-45. Epub 2003 Dec 11. PMID:14670977[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Roy C, Kester H, Visser J, Shevchik V, Hugouvieux-Cotte-Pattat N, Robert-Baudouy J, Benen J. Modes of action of five different endopectate lyases from Erwinia chrysanthemi 3937. J Bacteriol. 1999 Jun;181(12):3705-9. PMID:10368144 doi:10.1128/JB.181.12.3705-3709.1999
- ↑ Lojkowska E, Masclaux C, Boccara M, Robert-Baudouy J, Hugouvieux-Cotte-Pattat N. Characterization of the pelL gene encoding a novel pectate lyase of Erwinia chrysanthemi 3937. Mol Microbiol. 1995 Jun;16(6):1183-95. PMID:8577252 doi:10.1111/j.1365-2958.1995.tb02341.x
- ↑ Jenkins J, Shevchik VE, Hugouvieux-Cotte-Pattat N, Pickersgill RW. The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi. J Biol Chem. 2004 Mar 5;279(10):9139-45. Epub 2003 Dec 11. PMID:14670977 doi:10.1074/jbc.M311390200
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