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2plk

From Proteopedia

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{{Seed}}
 
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[[Image:2plk.png|left|200px]]
 
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==Crystal structure of lysine/ornithine decarboxylase complexed with cadaverine from Vibrio vulnificus==
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The line below this paragraph, containing "STRUCTURE_2plk", creates the "Structure Box" on the page.
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<StructureSection load='2plk' size='340' side='right'caption='[[2plk]], [[Resolution|resolution]] 2.14&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2plk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus_CMCP6 Vibrio vulnificus CMCP6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PLK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PLK FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.14&#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=P3D:(4-{(E)-[(5-AMINOPENTYL)IMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL+DIHYDROGEN+PHOSPHATE'>P3D</scene></td></tr>
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{{STRUCTURE_2plk| PDB=2plk | SCENE= }}
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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=2plk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2plk OCA], [https://pdbe.org/2plk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2plk RCSB], [https://www.ebi.ac.uk/pdbsum/2plk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2plk ProSAT]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pl/2plk_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2plk ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The beta/alpha-barrel fold type basic amino acid decarboxylases include eukaryotic ornithine decarboxylases (ODC) and bacterial and plant enzymes with activity on L-arginine and meso-diaminopimelate. These enzymes catalyze essential steps in polyamine and lysine biosynthesis. Phylogenetic analysis suggests that diverse bacterial species also contain ODC-like enzymes from this fold type. However, in comparison with the eukaryotic ODCs, amino acid differences were identified in the sequence of the 3(10)-helix that forms a key specificity element in the active site, suggesting they might function on novel substrates. Putative decarboxylases from a phylogenetically diverse range of bacteria were characterized to determine their substrate preference. Enzymes from species within Methanosarcina, Pseudomonas, Bartonella, Nitrosomonas, Thermotoga, and Aquifex showed a strong preference for L-ornithine, whereas the enzyme from Vibrio vulnificus (VvL/ODC) had dual specificity functioning well on both L-ornithine and L-lysine. The x-ray structure of VvL/ODC was solved in the presence of the reaction products putrescine and cadaverine to 1.7 and 2.15A, respectively. The overall structure is similar to eukaryotic ODC; however, reorientation of the 3(10)-helix enlarging the substrate binding pocket allows L-lysine to be accommodated. The structure of the putrescine-bound enzyme suggests that a bridging water molecule between the shorter L-ornithine and key active site residues provides the structural basis for VvL/ODC to also function on this substrate. Our data demonstrate that there is greater structural and functional diversity in bacterial polyamine biosynthetic decarboxylases than previously suspected.
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===Crystal structure of lysine/ornithine decarboxylase complexed with cadaverine from Vibrio vulnificus===
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Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases.,Lee J, Michael AJ, Martynowski D, Goldsmith EJ, Phillips MA J Biol Chem. 2007 Sep 14;282(37):27115-25. Epub 2007 Jul 11. PMID:17626020<ref>PMID:17626020</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2plk" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_17626020}}, adds the Publication Abstract to the page
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*[[Ornithine decarboxylase|Ornithine decarboxylase]]
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(as it appears on PubMed at http://www.pubmed.gov), where 17626020 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17626020}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2PLK is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PLK OCA].
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[[Category: Vibrio vulnificus CMCP6]]
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[[Category: Goldsmith EJ]]
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==Reference==
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[[Category: Lee J]]
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<ref group="xtra">PMID:17626020</ref><references group="xtra"/>
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[[Category: Phillips MA]]
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[[Category: Vibrio vulnificus]]
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[[Category: Goldsmith, E J.]]
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[[Category: Lee, J.]]
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[[Category: Phillips, M A.]]
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[[Category: Beta barrel]]
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[[Category: Beta/alpha barrel]]
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[[Category: Lyase]]
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[[Category: Type iv decarboxylase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 18:23:56 2009''
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Current revision

Crystal structure of lysine/ornithine decarboxylase complexed with cadaverine from Vibrio vulnificus

PDB ID 2plk

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