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| | <StructureSection load='3vee' size='340' side='right'caption='[[3vee]], [[Resolution|resolution]] 2.40Å' scene=''> | | <StructureSection load='3vee' size='340' side='right'caption='[[3vee]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3vee]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhojr Rhojr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VEE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3vee]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_jostii_RHA1 Rhodococcus jostii RHA1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VEE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <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]] 2.4Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vec|3vec]], [[3ved|3ved]], [[3vef|3vef]], [[3veg|3veg]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dypB, RHA1_ro02407 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=101510 RHOJR])</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=3vee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vee OCA], [https://pdbe.org/3vee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vee RCSB], [https://www.ebi.ac.uk/pdbsum/3vee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vee 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=3vee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vee OCA], [https://pdbe.org/3vee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vee RCSB], [https://www.ebi.ac.uk/pdbsum/3vee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vee ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/Q0SE24_RHOJR Q0SE24_RHOJR] |
| - | DypB from Rhodococcus jostii RHA1 is a bacterial dye-decolorizing peroxidase (DyP) that oxidizes lignin and Mn(II). Three residues interact with the iron-bound solvent species in ferric DypB: Asn-246 and the conserved Asp-153 and Arg-244. Substitution of either Asp-153 or Asn-246 with alanine minimally affected the second order rate constant for Compound I formation (k(1) approximately 10(5) M(-1)s(-1)) and the specificity constant (k(cat)/K(m)) for H(2)O(2). Even in the D153A/N246A double variant, these values were reduced less than 30-fold. However, these substitutions dramatically reduced the stability of Compound I (t(1/2) approximately 0.13 s) as compared with the wild-type enzyme (540 s). By contrast, substitution of Arg-244 with leucine abolished the peroxidase activity, and heme iron of the variant showed a pH-dependent transition from high spin (pH 5) to low spin (pH 8.5). Two variants were designed to mimic the plant peroxidase active site: D153H, which was more than an order of magnitude less reactive with H(2)O(2), and N246H, which had no detectable peroxidase activity. X-ray crystallographic studies revealed that structural changes in the variants are confined to the distal heme environment. The data establish an essential role for Arg-244 in Compound I formation in DypB, possibly through charge stabilization and proton transfer. The principle roles of Asp-153 and Asn-246 appear to be in modulating the subsequent reactivity of Compound I. These results expand the range of residues known to catalyze Compound I formation in heme peroxidases.
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| - | Distal heme pocket residues of B-type dye-decolorizing peroxidase: arginine but not aspartate is essential for peroxidase activity.,Singh R, Grigg JC, Armstrong Z, Murphy ME, Eltis LD J Biol Chem. 2012 Mar 23;287(13):10623-30. Epub 2012 Feb 3. PMID:22308037<ref>PMID:22308037</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 3vee" style="background-color:#fffaf0;"></div>
| + | |
| - | == References ==
| + | |
| - | <references/>
| + | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Rhojr]] | + | [[Category: Rhodococcus jostii RHA1]] |
| - | [[Category: Armstrong, Z]] | + | [[Category: Armstrong Z]] |
| - | [[Category: Eltis, L D]] | + | [[Category: Eltis LD]] |
| - | [[Category: Grigg, J C]] | + | [[Category: Grigg JC]] |
| - | [[Category: Murphy, M E.P]] | + | [[Category: Murphy MEP]] |
| - | [[Category: Singh, R]] | + | [[Category: Singh R]] |
| - | [[Category: Dyp]]
| + | |
| - | [[Category: Lignan]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Peroxidase]]
| + | |
