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| | <StructureSection load='5vj0' size='340' side='right'caption='[[5vj0]], [[Resolution|resolution]] 1.93Å' scene=''> | | <StructureSection load='5vj0' size='340' side='right'caption='[[5vj0]], [[Resolution|resolution]] 1.93Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5vj0]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"enterobacter_lignolyticus"_deangelis_et_al._2011 "enterobacter lignolyticus" deangelis et al. 2011]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VJ0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5vj0]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacter_lignolyticus Enterobacter lignolyticus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VJ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VJ0 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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]] 1.93Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">YfeX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1334193 "Enterobacter lignolyticus" Deangelis et al. 2011])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></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=5vj0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vj0 OCA], [http://pdbe.org/5vj0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vj0 RCSB], [http://www.ebi.ac.uk/pdbsum/5vj0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vj0 ProSAT]</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=5vj0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vj0 OCA], [https://pdbe.org/5vj0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vj0 RCSB], [https://www.ebi.ac.uk/pdbsum/5vj0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vj0 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/E3G9I4_ENTLS E3G9I4_ENTLS] |
| | <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: Enterobacter lignolyticus deangelis et al. 2011]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Geisbrecht, B V]] | + | [[Category: Geisbrecht BV]] |
| - | [[Category: Li, P]] | + | [[Category: Li P]] |
| - | [[Category: Meekins, D A]] | + | [[Category: Meekins DA]] |
| - | [[Category: Enterobacter lignolyticus]]
| + | |
| - | [[Category: Heme]]
| + | |
| - | [[Category: Lignin]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Peroxidase]]
| + | |
| Structural highlights
Function
E3G9I4_ENTLS
Publication Abstract from PubMed
Dye-decolorizing peroxidases (DyPs) are a family of H2O2-dependent heme peroxidases, which have shown potential applications in lignin degradation and valorization. However, the DyP kinetic mechanism remains underexplored. Using structural biology and solvent isotope (sKIE) and viscosity effects, many mechanistic characteristics have been uncovered for the B-class ElDyP from Enterobacter lignolyticus. Its structure revealed that a water molecule acts as the sixth axial ligand with two channels at diameters of ~3.0 and 8.0 A leading to the heme center. A conformational change of ERS(*) to ERS, which have identical spectral characteristics, was proposed as the final step in DyPs' bisubstrate Ping-Pong mechanism. This step is also the rate-determining step in ABTS oxidation. The normal KIE of wild-type ElDyP with D2O2 at pH 3.5 suggested that cmpd 0 deprotonation by the distal aspartate is rate-limiting in the formation of cmpd I, which is more reactive under acidic pH than under neutral or alkaline pH. The viscosity effects and other biochemical methods implied that the reducing substrate binds with cmpd I instead of the free enzyme. The significant inverse sKIEs of kcat/KM and kERS* suggested that the aquo release in DyPs is mechanistically important and may explain the enzyme's adoption of two-electron reduction for cmpd I. The distal aspartate is catalytically more important than the distal arginine and plays key roles in determining DyPs' acidic pH optimum. The kinetic mechanism of D143H-ElDyP was also briefly studied. The results obtained will pave the way for future protein engineering to improve DyPs' lignolytic activity.
Mechanistic Insights into Dye-Decolorizing Peroxidase Revealed by Solvent Isotope and Viscosity Effects.,Shrestha R, Huang G, Meekins DA, Geisbrecht BV, Li P ACS Catal. 2017 Sep 1;7(9):6352-6364. doi: 10.1021/acscatal.7b01861. Epub 2017, Aug 9. PMID:29308295[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Shrestha R, Huang G, Meekins DA, Geisbrecht BV, Li P. Mechanistic Insights into Dye-Decolorizing Peroxidase Revealed by Solvent Isotope and Viscosity Effects. ACS Catal. 2017 Sep 1;7(9):6352-6364. doi: 10.1021/acscatal.7b01861. Epub 2017, Aug 9. PMID:29308295 doi:http://dx.doi.org/10.1021/acscatal.7b01861
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