1plu: Difference between revisions

New page: left|200px<br /><applet load="1plu" size="450" color="white" frame="true" align="right" spinBox="true" caption="1plu, resolution 2.2Å" /> '''PECTATE LYASE C FROM ...
 
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'''PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI WITH 1 LU+3 ION IN THE PUTATIVE CALCIUM BINDING SITE'''<br />


==Overview==
==PECTATE LYASE C FROM ERWINIA CHRYSANTHEMI WITH 1 LU+3 ION IN THE PUTATIVE CALCIUM BINDING SITE==
The crystal structure of pectate lyase C (EC 4.2.2.2) from the, enterobacterium Erwinia chrysanthemi (PelC) has been refined by molecular, dynamics techniques to a resolution of 2.2 A to an R factor of 17.97%. The, final model consists of 352 of the total 353 amino acids and 114 solvent, molecules. The root-mean-square deviation from ideality is 0.009 A for, bond lengths and 1.768[deg] for bond angles. The structure of PelC bound, to the lanthanide ion lutetium, used as a calcium analog, has also been, refined. Lutetium inhibits the enzymatic activity of the protein, and in, the PelC-lutetium structure, the ion binds in the putative calcium-binding, site. Five side-chain atoms form ligands to the lutetium ion. An analysis, of the atomic-level model of the two protein structures reveals possible, implications for the enzymatic mechanism of the enzyme.
<StructureSection load='1plu' size='340' side='right'caption='[[1plu]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1plu]] 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=1PLU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PLU 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]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</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=1plu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1plu OCA], [https://pdbe.org/1plu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1plu RCSB], [https://www.ebi.ac.uk/pdbsum/1plu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1plu ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PLYC_DICCH PLYC_DICCH] Involved in maceration and soft-rotting of plant tissue.
== 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/pl/1plu_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=1plu ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of pectate lyase C (EC 4.2.2.2) from the enterobacterium Erwinia chrysanthemi (PelC) has been refined by molecular dynamics techniques to a resolution of 2.2 A to an R factor of 17.97%. The final model consists of 352 of the total 353 amino acids and 114 solvent molecules. The root-mean-square deviation from ideality is 0.009 A for bond lengths and 1.768[deg] for bond angles. The structure of PelC bound to the lanthanide ion lutetium, used as a calcium analog, has also been refined. Lutetium inhibits the enzymatic activity of the protein, and in the PelC-lutetium structure, the ion binds in the putative calcium-binding site. Five side-chain atoms form ligands to the lutetium ion. An analysis of the atomic-level model of the two protein structures reveals possible implications for the enzymatic mechanism of the enzyme.


==About this Structure==
The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism).,Yoder MD, Jurnak F Plant Physiol. 1995 Feb;107(2):349-364. PMID:12228363<ref>PMID:12228363</ref>
1PLU 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 LU 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=1PLU OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
The Refined Three-Dimensional Structure of Pectate Lyase C from Erwinia chrysanthemi at 2.2 Angstrom Resolution (Implications for an Enzymatic Mechanism)., Yoder MD, Jurnak F, Plant Physiol. 1995 Feb;107(2):349-364. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12228363 12228363]
</div>
[[Category: Erwinia chrysanthemi]]
<div class="pdbe-citations 1plu" style="background-color:#fffaf0;"></div>
[[Category: Pectate lyase]]
== References ==
[[Category: Single protein]]
<references/>
[[Category: Jurnak, F.A.]]
__TOC__
[[Category: Yoder, M.D.]]
</StructureSection>
[[Category: LU]]
[[Category: Dickeya chrysanthemi]]
[[Category: parallel beta-helix]]
[[Category: Large Structures]]
[[Category: pectate cleavage]]
[[Category: Jurnak FA]]
[[Category: pectinolytic activity]]
[[Category: Yoder MD]]
[[Category: trans-elimination]]
 
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