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1ru4

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(New page: 200px<br /><applet load="1ru4" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ru4, resolution 1.60&Aring;" /> '''Crystal structure of...)
Current revision (08:27, 1 May 2024) (edit) (undo)
 
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[[Image:1ru4.gif|left|200px]]<br /><applet load="1ru4" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ru4, resolution 1.60&Aring;" />
 
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'''Crystal structure of pectate lyase Pel9A'''<br />
 
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==Overview==
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==Crystal structure of pectate lyase Pel9A==
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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.
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<StructureSection load='1ru4' size='340' side='right'caption='[[1ru4]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<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>
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1RU4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Erwinia_chrysanthemi Erwinia chrysanthemi] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RU4 OCA].
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</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>
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<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>
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==Reference==
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<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>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14670977 14670977]
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</table>
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[[Category: Erwinia chrysanthemi]]
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== Function ==
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[[Category: Pectate lyase]]
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[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>
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[[Category: Single protein]]
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== Evolutionary Conservation ==
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[[Category: Hugouvieux-Cotte-Pattat, N.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Jenkins, J.]]
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Check<jmol>
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[[Category: Pickersgill, R.W.]]
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<jmolCheckbox>
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[[Category: Shevchik, V.E.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ru/1ru4_consurf.spt"</scriptWhenChecked>
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[[Category: CA]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: parallel beta-helix]]
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 01:52:11 2007''
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</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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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Dickeya chrysanthemi]]
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[[Category: Large Structures]]
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[[Category: Hugouvieux-Cotte-Pattat N]]
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[[Category: Jenkins J]]
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[[Category: Pickersgill RW]]
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[[Category: Shevchik VE]]

Current revision

Crystal structure of pectate lyase Pel9A

PDB ID 1ru4

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