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| | ==DyPB from Rhodococcus jostii RHA1, crystal form 2== | | ==DyPB from Rhodococcus jostii RHA1, crystal form 2== |
| - | <StructureSection load='3qns' size='340' side='right' caption='[[3qns]], [[Resolution|resolution]] 1.40Å' scene=''> | + | <StructureSection load='3qns' size='340' side='right'caption='[[3qns]], [[Resolution|resolution]] 1.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3qns]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhosr Rhosr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QNS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QNS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3qns]] is a 1 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=3QNS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QNS FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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]] 1.4Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3qnr|3qnr]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DyPB, RHA1_ro02407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=101510 RHOSR])</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=3qns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qns OCA], [https://pdbe.org/3qns PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qns RCSB], [https://www.ebi.ac.uk/pdbsum/3qns PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qns 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=3qns FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qns OCA], [http://pdbe.org/3qns PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3qns RCSB], [http://www.ebi.ac.uk/pdbsum/3qns PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3qns 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] |
| - | The soil bacterium Rhodococcus jostii RHA1 contains two dye-decolorizing peroxidases (DyPs) named according to the subfamily they represent: DypA, predicted to be periplasmic, and DypB, implicated in lignin degradation. Steady-state kinetic studies of these enzymes revealed that they have much lower peroxidase activities than C- and D-type DyPs. Nevertheless, DypA showed 6-fold greater apparent specificity for the anthraquinone dye Reactive Blue 4 (k(cat)/K(m) = 12800 +/- 600 M(-1) s(-1)) than either ABTS or pyrogallol, consistent with previously characterized DyPs. By contrast, DypB showed the greatest apparent specificity for ABTS (k(cat)/K(m) = 2000 +/- 100 M(-1) s(-1)) and also oxidized Mn(II) (k(cat)/K(m) = 25.1 +/- 0.1 M(-1) s(-1)). Further differences were detected using electron paramagnetic resonance (EPR) spectroscopy: while both DyPs contained high-spin (S = (5)/(2)) Fe(III) in the resting state, DypA had a rhombic high-spin signal (g(y) = 6.32, g(x) = 5.45, and g(z) = 1.97) while DypB had a predominantly axial signal (g(y) = 6.09, g(x) = 5.45, and g(z) = 1.99). Moreover, DypA reacted with H(2)O(2) to generate an intermediate with features of compound II (Fe(IV) horizontal lineO). By contrast, DypB reacted with H(2)O(2) with a second-order rate constant of (1.79 +/- 0.06) x 10(5) M(-1) s(-1) to generate a relatively stable green-colored intermediate (t(1/2) approximately 9 min). While the electron absorption spectrum of this intermediate was similar to that of compound I of plant-type peroxidases, its EPR spectrum was more consistent with a poorly coupled protein-based radical than with an [Fe(IV) horizontal lineO Por(*)](+) species. The X-ray crystal structure of DypB, determined to 1.4 A resolution, revealed a hexacoordinated heme iron with histidine and a solvent species occupying axial positions. A solvent channel potentially provides access to the distal face of the heme for H(2)O(2). A shallow pocket exposes heme propionates to the solvent and contains a cluster of acidic residues that potentially bind Mn(II). Insight into the structure and function of DypB facilitates its engineering for the improved degradation of lignocellulose.
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| - | Characterization of dye-decolorizing peroxidases from Rhodococcus jostii RHA1.,Roberts JN, Singh R, Grigg JC, Murphy ME, Bugg TD, Eltis LD Biochemistry. 2011 Jun 14;50(23):5108-19. Epub 2011 May 19. PMID:21534572<ref>PMID:21534572</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 3qns" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Rhosr]] | + | [[Category: Large Structures]] |
| - | [[Category: Eltis, L D]] | + | [[Category: Rhodococcus jostii RHA1]] |
| - | [[Category: Grigg, J C]] | + | [[Category: Eltis LD]] |
| - | [[Category: Murphy, M E.P]] | + | [[Category: Grigg JC]] |
| - | [[Category: Roberts, J N]] | + | [[Category: Murphy MEP]] |
| - | [[Category: Singh, R]] | + | [[Category: Roberts JN]] |
| - | [[Category: Dyp]] | + | [[Category: Singh R]] |
| - | [[Category: Enzyme]]
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| - | [[Category: Heme]]
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| - | [[Category: Lignan]]
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| - | [[Category: Oxidoreductase]]
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| - | [[Category: Peroxidase]]
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