2d3q: Difference between revisions

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[[Image:2d3q.gif|left|200px]]


{{Structure
==Crystal Structure of a Decolorizing Peroxidase (DyP) That Catalyses the Biological Oxidation of Anthraquinone Derivatives==
|PDB= 2d3q |SIZE=350|CAPTION= <scene name='initialview01'>2d3q</scene>, resolution 2.8&Aring;
<StructureSection load='2d3q' size='340' side='right'caption='[[2d3q]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>
<table><tr><td colspan='2'>[[2d3q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bjerkandera_adusta Bjerkandera adusta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3Q FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
|GENE=  
<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>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3q OCA], [https://pdbe.org/2d3q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3q RCSB], [https://www.ebi.ac.uk/pdbsum/2d3q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3q ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d3q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3q OCA], [http://www.ebi.ac.uk/pdbsum/2d3q PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2d3q RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/Q8WZK8_9APHY Q8WZK8_9APHY]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d3/2d3q_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d3q ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The dye-decolorizing peroxidase (DyP)-type peroxidase family is a unique heme peroxidase family. The primary and tertiary structures of this family are obviously different from those of other heme peroxidases. However, the details of the structure-function relationships of this family remain poorly understood. We show four high-resolution structures of DyP (EC1.11.1.19), which is representative of this family: the native DyP (1.40 A), the D171N mutant DyP (1.42 A), the native DyP complexed with cyanide (1.45 A), and the D171N mutant DyP associated with cyanide (1.40 A). These structures contain four amino acids forming the binding pocket for hydrogen peroxide, and they are remarkably conserved in this family. Moreover, these structures show that OD2 of Asp171 accepts a proton from hydrogen peroxide in compound I formation, and that OD2 can swing to the appropriate position in response to the ligand for heme iron. On the basis of these results, we propose a swing mechanism in compound I formation. When DyP reacts with hydrogen peroxide, OD2 swings towards an optimal position to accept the proton from hydrogen peroxide bound to the heme iron.


'''Crystal Structure of a Decolorizing Peroxidase (DyP) That Catalyses the Biological Oxidation of Anthraquinone Derivatives'''
The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue.,Yoshida T, Tsuge H, Konno H, Hisabori T, Sugano Y FEBS J. 2011 Jul;278(13):2387-94. doi: 10.1111/j.1742-4658.2011.08161.x., Epub 2011 May 31. PMID:21569205<ref>PMID:21569205</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==Overview==
</div>
The dye-decolorizing peroxidase DyP is a key enzyme in the decolorizing fungus Thanatephorus cucumeris Dec 1 that degrades azo and antraquinone dyes. The gene dyp from T. cucumeris Dec 1, which has low homology to other peroxidase genes, was cloned and transformed into Aspergillus oryzae and glycosylated DyP was expressed at high levels. Purified DyP was deglycosylated using GST Endo F1 and then crystallized in a strong magnetic field (10 T) at 283 K using ammonium sulfate as precipitant. X-ray diffraction data to 2.96 A resolution collected from a native crystal at the Photon Factory (Tsukuba, Japan) showed that the crystal belonged to the hexagonal space group P6(5)22, with unit-cell parameters a = b = 136.15, c = 363.46 A. The asymmetric unit of the crystal contained four DyP molecules, with a corresponding Matthews coefficient (V(M)) of 2.50 A(3) Da(-1) and a solvent content of 51%. Heavy-atom derivatives of DyP have been obtained and electron-density maps have been calculated. The haem is visible and continuous electron density between the haem and protein clearly indicates the location of the proximal histidine ligand.
<div class="pdbe-citations 2d3q" style="background-color:#fffaf0;"></div>
 
== References ==
==About this Structure==
<references/>
2D3Q is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thanatephorus_cucumeris Thanatephorus cucumeris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3Q OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Bjerkandera adusta]]
A unique dye-decolorizing peroxidase, DyP, from Thanatephorus cucumeris Dec 1: heterologous expression, crystallization and preliminary X-ray analysis., Sato T, Hara S, Matsui T, Sazaki G, Saijo S, Ganbe T, Tanaka N, Sugano Y, Shoda M, Acta Crystallogr D Biol Crystallogr. 2004 Jan;60(Pt 1):149-52. Epub 2003, Dec 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14684913 14684913]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Sato T]]
[[Category: Thanatephorus cucumeris]]
[[Category: Shoda M]]
[[Category: Sato, T.]]
[[Category: Sugano Y]]
[[Category: Shoda, M.]]
[[Category: Sugano, Y.]]
[[Category: strands and helix]]
 
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Retrieved from "https://proteopedia.org/2d3q"