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[[ | ==The crystal structures of several mutants of pleurotus eryngii versatile peroxidase== | ||
<StructureSection load='4fdq' size='340' side='right' caption='[[4fdq]], [[Resolution|resolution]] 1.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4fdq]] is a 1 chain structure with 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=4FDQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FDQ 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> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fcs|4fcs]], [[4fcn|4fcn]], [[4fef|4fef]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">vpl2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5323 Pleurotus eryngii])</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4fdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fdq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4fdq RCSB], [http://www.ebi.ac.uk/pdbsum/4fdq PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Versatile peroxidase shares with manganese peroxidase and lignin peroxidase the ability to oxidize Mn(2+) and high redox potential aromatic compounds, respectively. Moreover, it is also able to oxidize phenols (and low redox potential dyes) at two catalytic sites, as shown by biphasic kinetics. A high efficiency site (with 2,6-dimethoxyphenol and p-hydroquinone catalytic efficiencies of approximately 70 and approximately 700 s(-1) mm(-1), respectively) was localized at the same exposed Trp-164 responsible for high redox potential substrate oxidation (as shown by activity loss in the W164S variant). The second site, characterized by low catalytic efficiency ( approximately 3 and approximately 50 s(-1) mm(-1) for 2,6-dimethoxyphenol and p-hydroquinone, respectively) was localized at the main heme access channel. Steady-state and transient-state kinetics for oxidation of phenols and dyes at the latter site were improved when side chains of residues forming the heme channel edge were removed in single and multiple variants. Among them, the E140G/K176G, E140G/P141G/K176G, and E140G/W164S/K176G variants attained catalytic efficiencies for oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) at the heme channel similar to those of the exposed tryptophan site. The heme channel enlargement shown by x-ray diffraction of the E140G, P141G, K176G, and E140G/K176G variants would allow a better substrate accommodation near the heme, as revealed by the up to 26-fold lower K(m) values (compared with native VP). The resulting interactions were shown by the x-ray structure of the E140G-guaiacol complex, which includes two H-bonds of the substrate with Arg-43 and Pro-139 in the distal heme pocket (at the end of the heme channel) and several hydrophobic interactions with other residues and the heme cofactor. | |||
Two Oxidation Sites for Low Redox Potential Substrates: A DIRECTED MUTAGENESIS, KINETIC, AND CRYSTALLOGRAPHIC STUDY ON PLEUROTUS ERYNGII VERSATILE PEROXIDASE.,Morales M, Mate MJ, Romero A, Martinez MJ, Martinez AT, Ruiz-Duenas FJ J Biol Chem. 2012 Nov 30;287(49):41053-67. doi: 10.1074/jbc.M112.405548. Epub, 2012 Oct 15. PMID:23071108<ref>PMID:23071108</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | |||
< | |||
[[Category: Pleurotus eryngii]] | [[Category: Pleurotus eryngii]] | ||
[[Category: Versatile peroxidase]] | [[Category: Versatile peroxidase]] | ||
[[Category: Martinez, A T | [[Category: Martinez, A T]] | ||
[[Category: Mate, M J | [[Category: Mate, M J]] | ||
[[Category: Romero, A | [[Category: Romero, A]] | ||
[[Category: Ruiz-Duenas, F J | [[Category: Ruiz-Duenas, F J]] | ||
[[Category: Aromatic-substrate binding]] | [[Category: Aromatic-substrate binding]] | ||
[[Category: Lignin degradation]] | [[Category: Lignin degradation]] | ||
[[Category: Lignin peroxidase]] | [[Category: Lignin peroxidase]] | ||
[[Category: Oxidoreductase]] | [[Category: Oxidoreductase]] | ||
Revision as of 19:02, 9 December 2014
The crystal structures of several mutants of pleurotus eryngii versatile peroxidaseThe crystal structures of several mutants of pleurotus eryngii versatile peroxidase
Structural highlights
Publication Abstract from PubMedVersatile peroxidase shares with manganese peroxidase and lignin peroxidase the ability to oxidize Mn(2+) and high redox potential aromatic compounds, respectively. Moreover, it is also able to oxidize phenols (and low redox potential dyes) at two catalytic sites, as shown by biphasic kinetics. A high efficiency site (with 2,6-dimethoxyphenol and p-hydroquinone catalytic efficiencies of approximately 70 and approximately 700 s(-1) mm(-1), respectively) was localized at the same exposed Trp-164 responsible for high redox potential substrate oxidation (as shown by activity loss in the W164S variant). The second site, characterized by low catalytic efficiency ( approximately 3 and approximately 50 s(-1) mm(-1) for 2,6-dimethoxyphenol and p-hydroquinone, respectively) was localized at the main heme access channel. Steady-state and transient-state kinetics for oxidation of phenols and dyes at the latter site were improved when side chains of residues forming the heme channel edge were removed in single and multiple variants. Among them, the E140G/K176G, E140G/P141G/K176G, and E140G/W164S/K176G variants attained catalytic efficiencies for oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) at the heme channel similar to those of the exposed tryptophan site. The heme channel enlargement shown by x-ray diffraction of the E140G, P141G, K176G, and E140G/K176G variants would allow a better substrate accommodation near the heme, as revealed by the up to 26-fold lower K(m) values (compared with native VP). The resulting interactions were shown by the x-ray structure of the E140G-guaiacol complex, which includes two H-bonds of the substrate with Arg-43 and Pro-139 in the distal heme pocket (at the end of the heme channel) and several hydrophobic interactions with other residues and the heme cofactor. Two Oxidation Sites for Low Redox Potential Substrates: A DIRECTED MUTAGENESIS, KINETIC, AND CRYSTALLOGRAPHIC STUDY ON PLEUROTUS ERYNGII VERSATILE PEROXIDASE.,Morales M, Mate MJ, Romero A, Martinez MJ, Martinez AT, Ruiz-Duenas FJ J Biol Chem. 2012 Nov 30;287(49):41053-67. doi: 10.1074/jbc.M112.405548. Epub, 2012 Oct 15. PMID:23071108[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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