This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2vka

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

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

Structural highlights

2vka is a 1 chain structure with sequence from Pleurotus eryngii. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VPL2_PLEER A versatile ligninolytic peroxidase that combines the substrate specificity characteristics of the two other ligninolytic peroxidases, manganese peroxidase and lignin peroxidase.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Ruiz-Duenas FJ, Martinez MJ, Martinez AT. Molecular characterization of a novel peroxidase isolated from the ligninolytic fungus Pleurotus eryngii. Mol Microbiol. 1999 Jan;31(1):223-35. PMID:9987124
↑ Ruiz-Duenas FJ, Morales M, Mate MJ, Romero A, Martinez MJ, Smith AT, Martinez AT. Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii Versatile Peroxidase(,). Biochemistry. 2008 Feb 12;47(6):1685-95. Epub 2008 Jan 18. PMID:18201105 doi:10.1021/bi7020298

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2vka"

@@ Line 1: / Line 1: @@
-==SITE-DIRECTED MUTAGENESIS OF THE CATALYTIC TRYPTOPHAN ENVIRONMENT IN PLEUROTUS ERYNGII VERSATILE PEROXIDASE==
-<StructureSection load='2vka' size='340' side='right' caption='[[2vka]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+==Site-Directed Mutagenesis of the Catalytic Tryptophan Environment in Pleurotus eryngii Versatile Peroxidase==
+<StructureSection load='2vka' size='340' side='right'caption='[[2vka]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2vka]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Boletus_of_the_steppes Boletus of the steppes]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VKA FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2boq|2boq]]</td></tr>
+<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>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Versatile_peroxidase Versatile peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.16 1.11.1.16] </span></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=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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vka FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vka OCA], [http://pdbe.org/2vka PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vka RCSB], [http://www.ebi.ac.uk/pdbsum/2vka PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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>
 == 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/vk/2vka_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vk/2vka_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Boletus of the steppes]]
+[[Category: Large Structures]]
-[[Category: Versatile peroxidase]]
+[[Category: Pleurotus eryngii]]
-[[Category: Martinez, A T]]
+[[Category: Martinez AT]]
-[[Category: Martinez, M J]]
+[[Category: Martinez MJ]]
-[[Category: Mate, M J]]
+[[Category: Mate MJ]]
-[[Category: Morales, M]]
+[[Category: Morales M]]
-[[Category: Romero, A]]
+[[Category: Romero A]]
-[[Category: Ruiz-Duenas, F J]]
+[[Category: Ruiz-Duenas FJ]]
-[[Category: Smith, A]]
+[[Category: Smith A]]
-[[Category: Aromatic-substrate binding]]
-[[Category: Lignin degradation]]
-[[Category: Lignin peroxidase]]
-[[Category: Manganese peroxidase]]
-[[Category: Mn-independent oxidation]]
-[[Category: Oxidoreductase]]
-[[Category: Polyvalent peroxidase]]

2vka

From Proteopedia

Current revision

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox