5twt: Difference between revisions
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==Characterization of class III peroxidase from switchgrass (Panicum virgatum)== | ==Characterization of class III peroxidase from switchgrass (Panicum virgatum)== | ||
<StructureSection load='5twt' size='340' side='right' caption='[[5twt]], [[Resolution|resolution]] 1.30Å' scene=''> | <StructureSection load='5twt' size='340' side='right'caption='[[5twt]], [[Resolution|resolution]] 1.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5twt]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TWT OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5twt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Panicum_virgatum Panicum virgatum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TWT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TWT 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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.296Å</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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5twt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5twt OCA], [https://pdbe.org/5twt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5twt RCSB], [https://www.ebi.ac.uk/pdbsum/5twt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5twt ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A1S4NYF8_PANVG A0A1S4NYF8_PANVG] Removal of H(2)O(2), oxidation of toxic reductants, biosynthesis and degradation of lignin, suberization, auxin catabolism, response to environmental stresses such as wounding, pathogen attack and oxidative stress.[RuleBase:RU362060] | |||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
== Publication Abstract from PubMed == | == Publication Abstract from PubMed == | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Panicum virgatum]] | ||
[[Category: | [[Category: Kang C]] | ||
[[Category: | [[Category: Moural TW]] | ||
Latest revision as of 16:15, 4 October 2023
Characterization of class III peroxidase from switchgrass (Panicum virgatum)Characterization of class III peroxidase from switchgrass (Panicum virgatum)
Structural highlights
FunctionA0A1S4NYF8_PANVG Removal of H(2)O(2), oxidation of toxic reductants, biosynthesis and degradation of lignin, suberization, auxin catabolism, response to environmental stresses such as wounding, pathogen attack and oxidative stress.[RuleBase:RU362060] Publication Abstract from PubMedClass III peroxidases (CIIIPRX) catalyze the oxidation of monolignols, generate radicals, and ultimately lead to the formation of lignin. In general, CIIIPRX genes encode a large number of isozymes with ranges of in vitro substrate specificities. In order to elucidate the mode of substrate specificity of these enzymes, we characterized one of the CIIIPRXs (PviPRX9) from switchgrass (Panicum virgatum), a strategic plant for second-generation biofuels. The crystal structure, kinetic experiments, molecular docking, as well as expression patterns of PviPRX9 across multiple tissues and treatments, along with its levels of coexpression with the majority of genes in the monolignol biosynthesis pathway, revealed the function of PviPRX9 in lignification. Significantly, our study suggested that PviPRX9 has the ability to oxidize a broad range of phenylpropanoids with rather similar efficiencies, which reflects its role in the fortification of cell walls during normal growth and root development and in response to insect feeding. Based on the observed interactions of phenylpropanoids in the active site and analysis of kinetics, a catalytic mechanism involving two water molecules and residues histidine-42, arginine-38, and serine-71 was proposed. In addition, proline-138 and gluntamine-140 at the 137P-X-P-X140 motif, leucine-66, proline-67, and asparagine-176 may account for the broad substrate specificity of PviPRX9. Taken together, these observations shed new light on the function and catalysis of PviPRX9 and potentially benefit efforts to improve biomass conservation properties in bioenergy and forage crops. Characterization of Class III Peroxidases from Switchgrass.,Moural TW, Lewis KM, Barnaba C, Zhu F, Palmer NA, Sarath G, Scully ED, Jones JP, Sattler SE, Kang C Plant Physiol. 2017 Jan;173(1):417-433. doi: 10.1104/pp.16.01426. Epub 2016 Nov, 15. PMID:27879392[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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