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2vtv

From Proteopedia

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[[Image:2vtv.png|left|200px]]
 
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==PhaZ7 depolymerase from Paucimonas lemoignei==
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The line below this paragraph, containing "STRUCTURE_2vtv", creates the "Structure Box" on the page.
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<StructureSection load='2vtv' size='340' side='right'caption='[[2vtv]], [[Resolution|resolution]] 1.90&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'>[[2vtv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Paucimonas_lemoignei Paucimonas lemoignei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VTV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VTV FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
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-->
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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=2vtv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vtv OCA], [https://pdbe.org/2vtv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vtv RCSB], [https://www.ebi.ac.uk/pdbsum/2vtv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vtv ProSAT]</span></td></tr>
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{{STRUCTURE_2vtv| PDB=2vtv | SCENE= }}
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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/vt/2vtv_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=2vtv 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 crystal structure of poly(3-hydroxybutyrate) (PHB) depolymerase PhaZ7 purified from Paucimonas lemoignei was determined at 1.90 A resolution. The structure consists of a single domain with an alpha/beta hydrolase fold in its core. The active site is analogous to that of serine esterases/lipases and is characterized by the presence of a catalytic triad comprising Ser136, Asp242, and His306. Comparison with other structures in the Protein Data Bank showed a high level of similarity with the Bacillus subtilis lipase LipA (RMSD, 1.55 A). Structural comparison with Penicillium funiculosum PHB depolymerase, the only PHB depolymerase whose structure is already known, revealed significant differences, resulting in an RMSD of 2.80-3.58 A. The two enzymes appear to utilize different types of solvent-exposed residues for biopolymer binding, with aliphatic and hydroxyl residues used in P. funiculosum PHB depolymerase and aromatic residues in PhaZ7. Moreover, the active site of P. funiculosum PHB depolymerase is accessible to the substrate in contrast to the active site of PhaZ7, which is buried. Hence, considerable conformational changes are required in PhaZ7 for the creation of a channel leading to the active site. Taken together, the structural data suggest that PhaZ7 and P. funiculosum PHB depolymerase have adopted different strategies for effective substrate binding in response to their diverse substrate specificity and the lack of a substrate-binding domain.
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===PHAZ7 DEPOLYMERASE FROM PAUCIMONAS LEMOIGNEI===
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Structural basis of poly(3-hydroxybutyrate) hydrolysis by PhaZ7 depolymerase from Paucimonas lemoignei.,Papageorgiou AC, Hermawan S, Singh CB, Jendrossek D J Mol Biol. 2008 Oct 24;382(5):1184-94. Epub 2008 Aug 5. PMID:18706425<ref>PMID:18706425</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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<!--
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_18706425}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2vtv" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18706425 is the PubMed ID number.
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== References ==
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-->
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<references/>
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{{ABSTRACT_PUBMED_18706425}}
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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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[[2vtv]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VTV OCA].
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[[Category: Paucimonas lemoignei]]
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[[Category: Hermawan, S]]
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==Reference==
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[[Category: Jendrossek, D]]
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<ref group="xtra">PMID:18706425</ref><ref group="xtra">PMID:16511073</ref><references group="xtra"/>
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[[Category: Papageorgiou, A C]]
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[[Category: Hermawan, S.]]
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[[Category: Singh, C B]]
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[[Category: Jendrossek, D.]]
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[[Category: Papageorgiou, A C.]]
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[[Category: Singh, C B.]]
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[[Category: Hydrolase]]
[[Category: Hydrolase]]
[[Category: Polymerase]]
[[Category: Polymerase]]

Current revision

PhaZ7 depolymerase from Paucimonas lemoignei

PDB ID 2vtv

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