2vka

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{{Seed}}
 
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[[Image:2vka.png|left|200px]]
 
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==Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii Versatile Peroxidase==
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The line below this paragraph, containing "STRUCTURE_2vka", creates the "Structure Box" on the page.
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<StructureSection load='2vka' size='340' side='right'caption='[[2vka]], [[Resolution|resolution]] 2.00&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'>[[2vka]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pleurotus_eryngii Pleurotus eryngii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VKA 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&#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>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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{{STRUCTURE_2vka| PDB=2vka | 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=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [https://pdbe.org/2vka PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [https://www.ebi.ac.uk/pdbsum/2vka PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vka ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/VPL2_PLEER VPL2_PLEER] A versatile ligninolytic peroxidase that combines the substrate specificity characteristics of the two other ligninolytic peroxidases, manganese peroxidase and lignin peroxidase.<ref>PMID:9987124</ref>
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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/vk/2vka_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2vka 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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Lignin degradation by fungal peroxidases is initiated by one-electron transfer to an exposed tryptophan radical, a reaction mediated by veratryl alcohol (VA) in lignin peroxidase (LiP). Versatile peroxidase (VP) differs not only in its oxidation of Mn2+ at a second catalytic site but also in its ability to directly oxidize different aromatic compounds. The catalytic tryptophan environment was compared in LiP and VP crystal structures, and six residues near VP Trp164 were modified by site-directed mutagenesis. Oxidation of Mn2+ was practically unaffected. However, several mutations modified the oxidation kinetics of the high-redox-potential substrates VA and Reactive Black 5 (RB5), demonstrating that other residues contribute to substrate oxidation by the Trp164 radical. Introducing acidic residues at the tryptophan environment did not increase the efficiency of VP oxidizing VA. On the contrary, all variants harboring the R257D mutation lost their activity on RB5. Interestingly, this activity was restored when VA was added as a mediator, revealing the LiP-type behavior of this variant. Moreover, combination of the A260F and R257A mutations strongly increased (20-50-fold) the apparent second-order rate constants for reduction of VP compounds I and II by VA to values similar to those found in LiP. Dissociation of the enzyme-product complex seemed to be the limiting step in the turnover of this improved variant. Nonexposed residues in the vicinity of Trp164 can also affect VP activity, as found with the M247F mutation. This was a direct effect since no modification of the surrounding residues was found in the crystal structure of this variant.
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===SITE-DIRECTED MUTAGENESIS OF THE CATALYTIC TRYPTOPHAN ENVIRONMENT IN PLEUROTUS ERYNGII VERSATILE PEROXIDASE===
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Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii Versatile Peroxidase(,).,Ruiz-Duenas FJ, Morales M, Mate MJ, Romero A, Martinez MJ, Smith AT, Martinez AT Biochemistry. 2008 Feb 12;47(6):1685-95. Epub 2008 Jan 18. PMID:18201105<ref>PMID:18201105</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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The line below this paragraph, {{ABSTRACT_PUBMED_18201105}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2vka" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 18201105 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18201105}}
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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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2VKA is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pleurotus_eryngii Pleurotus eryngii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VKA OCA].
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==Reference==
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Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii Versatile Peroxidase(,)., Ruiz-Duenas FJ, Morales M, Mate MJ, Romero A, Martinez MJ, Smith AT, Martinez AT, Biochemistry. 2008 Feb 12;47(6):1685-95. Epub 2008 Jan 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18201105 18201105]
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[[Category: Pleurotus eryngii]]
[[Category: Pleurotus eryngii]]
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[[Category: Single protein]]
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[[Category: Martinez AT]]
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[[Category: Martinez, A T.]]
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[[Category: Martinez MJ]]
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[[Category: Martinez, M J.]]
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[[Category: Mate MJ]]
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[[Category: Mate, M J.]]
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[[Category: Morales M]]
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[[Category: Morales, M.]]
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[[Category: Romero A]]
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[[Category: Romero, A.]]
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[[Category: Ruiz-Duenas FJ]]
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[[Category: Ruiz-Duenas, F J.]]
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[[Category: Smith A]]
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[[Category: Smith, A.]]
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[[Category: Allelic variant]]
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[[Category: Aromatic-substrate binding]]
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[[Category: Electron transfer]]
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[[Category: Homology modeling]]
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[[Category: Lignin degradation]]
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[[Category: Lignin peroxidase]]
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[[Category: Manganese peroxidase]]
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[[Category: Mn-independent oxidation phenolic non-phenolic aromatic]]
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[[Category: Mnii oxidation]]
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[[Category: Oxidoreductase]]
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[[Category: Peroxidase]]
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[[Category: Polyvalent peroxidase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 09:24:24 2008''
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Current revision

Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii Versatile Peroxidase

PDB ID 2vka

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