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6yrd

From Proteopedia

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Current revision (07:40, 1 May 2024) (edit) (undo)
 
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<StructureSection load='6yrd' size='340' side='right'caption='[[6yrd]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
<StructureSection load='6yrd' size='340' side='right'caption='[[6yrd]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6yrd]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_lividans_1326 Streptomyces lividans 1326]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YRD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YRD FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6yrd]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_lividans_1326 Streptomyces lividans 1326]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YRD FirstGlance]. <br>
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</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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SAMN05428941_7146 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1200984 Streptomyces lividans 1326])</td></tr>
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<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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6yrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yrd OCA], [http://pdbe.org/6yrd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yrd RCSB], [http://www.ebi.ac.uk/pdbsum/6yrd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yrd ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6yrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yrd OCA], [https://pdbe.org/6yrd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yrd RCSB], [https://www.ebi.ac.uk/pdbsum/6yrd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yrd ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A0A1H2DDB9_9ACTN A0A1H2DDB9_9ACTN]
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Obtaining structures of intact redox states of metal centers derived from zero dose X-ray crystallography can advance our mechanistic understanding of metalloenzymes. In dye-decolorising heme peroxidases (DyPs), controversy exists regarding the mechanistic role of the distal heme residues aspartate and arginine in the heterolysis of peroxide to form the catalytic intermediate compound I (Fe(IV) =O and a porphyrin cation radical). Using serial femtosecond X-ray crystallography (SFX), we have determined the pristine structures of the Fe(III) and Fe(IV) =O redox states of a B-type DyP. These structures reveal a water-free distal heme site that, together with the presence of an asparagine, imply the use of the distal arginine as a catalytic base. A combination of mutagenesis and kinetic studies corroborate such a role. Our SFX approach thus provides unique insight into how the distal heme site of DyPs can be tuned to select aspartate or arginine for the rate enhancement of peroxide heterolysis.
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Serial Femtosecond Zero Dose Crystallography Captures a Water-Free Distal Heme Site in a Dye-Decolorising Peroxidase to Reveal a Catalytic Role for an Arginine in Fe(IV) =O Formation.,Lucic M, Svistunenko DA, Wilson MT, Chaplin AK, Davy B, Ebrahim A, Axford D, Tosha T, Sugimoto H, Owada S, Dworkowski FSN, Tews I, Owen RL, Hough MA, Worrall JAR Angew Chem Int Ed Engl. 2020 Nov 23;59(48):21656-21662. doi:, 10.1002/anie.202008622. Epub 2020 Sep 23. PMID:32780931<ref>PMID:32780931</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6yrd" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Streptomyces lividans 1326]]
[[Category: Streptomyces lividans 1326]]
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[[Category: Axford, D A]]
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[[Category: Axford DA]]
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[[Category: Hough, M A]]
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[[Category: Hough MA]]
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[[Category: Lucic, M]]
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[[Category: Lucic M]]
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[[Category: Owen, R L]]
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[[Category: Owen RL]]
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[[Category: Worrall, J A.R]]
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[[Category: Worrall JAR]]
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[[Category: Damage-free]]
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[[Category: Dye-decolourising]]
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[[Category: Ferryl]]
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[[Category: Oxidoreductase]]
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[[Category: Peroxidase]]
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[[Category: Serial femtosecond crystallography]]
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Current revision

SFX structure of dye-type peroxidase DtpB in the ferryl state

PDB ID 6yrd

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