6yr4: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
Line 3: Line 3:
<StructureSection load='6yr4' size='340' side='right'caption='[[6yr4]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
<StructureSection load='6yr4' size='340' side='right'caption='[[6yr4]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6yr4]] 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=6YR4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YR4 FirstGlance]. <br>
<table><tr><td colspan='2'>[[6yr4]] 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=6YR4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YR4 FirstGlance]. <br>
</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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.85&#8491;</td></tr>
<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>
<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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6yr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yr4 OCA], [http://pdbe.org/6yr4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yr4 RCSB], [http://www.ebi.ac.uk/pdbsum/6yr4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yr4 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=6yr4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yr4 OCA], [https://pdbe.org/6yr4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yr4 RCSB], [https://www.ebi.ac.uk/pdbsum/6yr4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yr4 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/A0A1H2DDB9_9ACTN A0A1H2DDB9_9ACTN]
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6yr4" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Streptomyces lividans 1326]]
[[Category: Streptomyces lividans 1326]]
[[Category: Dworkowski, F S.N]]
[[Category: Dworkowski FSN]]
[[Category: Hough, M A]]
[[Category: Hough MA]]
[[Category: Lucic, M]]
[[Category: Lucic M]]
[[Category: Worrall, J A.R]]
[[Category: Worrall JAR]]
[[Category: Dtpb]]
[[Category: Dye-decolourising]]
[[Category: Oxidoreductase]]
[[Category: Peroxidase]]
[[Category: Spectroscopically-validated]]

Latest revision as of 10:40, 1 May 2024

Dye-type peroxidase DtpB in the ferryl state: Spectroscopically Validated composite structureDye-type peroxidase DtpB in the ferryl state: Spectroscopically Validated composite structure

Structural highlights

6yr4 is a 6 chain structure with sequence from Streptomyces lividans 1326. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.85Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A1H2DDB9_9ACTN

6yr4, resolution 1.85Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=6yr4&oldid=4138654"