View source for 1ru4


==Crystal structure of pectate lyase Pel9A==
<StructureSection load='1ru4' size='340' side='right'caption='[[1ru4]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
<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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#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=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>
</table>
== Function ==
[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 ==
[[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/ru/1ru4_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=1ru4 ConSurf].
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== 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<ref>PMID:14670977</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1ru4" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Dickeya chrysanthemi]]
[[Category: Large Structures]]
[[Category: Hugouvieux-Cotte-Pattat N]]
[[Category: Jenkins J]]
[[Category: Pickersgill RW]]
[[Category: Shevchik VE]]