2d3q

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:46, 13 March 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2d3q.gif|left|200px]]<br /><applet load="2d3q" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="2d3q, resolution 2.8&Aring;" />
 
-
'''Crystal Structure of a Decolorizing Peroxidase (DyP) That Catalyses the Biological Oxidation of Anthraquinone Derivatives'''<br />
 
-
==Overview==
+
==Crystal Structure of a Decolorizing Peroxidase (DyP) That Catalyses the Biological Oxidation of Anthraquinone Derivatives==
-
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.
+
<StructureSection load='2d3q' size='340' side='right'caption='[[2d3q]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<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>
-
2D3Q is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thanatephorus_cucumeris Thanatephorus cucumeris] with <scene name='pdbligand=HEM:'>HEM</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D3Q OCA].
+
</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>
-
 
+
<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>
-
==Reference==
+
<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>
-
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=14684913 14684913]
+
</table>
-
[[Category: Single protein]]
+
== Function ==
-
[[Category: Thanatephorus cucumeris]]
+
[https://www.uniprot.org/uniprot/Q8WZK8_9APHY Q8WZK8_9APHY]
-
[[Category: Sato, T.]]
+
== Evolutionary Conservation ==
-
[[Category: Shoda, M.]]
+
[[Image:Consurf_key_small.gif|200px|right]]
-
[[Category: Sugano, Y.]]
+
Check<jmol>
-
[[Category: HEM]]
+
<jmolCheckbox>
-
[[Category: strands and helix]]
+
<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/initialview01.spt</scriptWhenUnchecked>
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:55:08 2008''
+
<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>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Bjerkandera adusta]]
 +
[[Category: Large Structures]]
 +
[[Category: Sato T]]
 +
[[Category: Shoda M]]
 +
[[Category: Sugano Y]]

Current revision

Crystal Structure of a Decolorizing Peroxidase (DyP) That Catalyses the Biological Oxidation of Anthraquinone Derivatives

PDB ID 2d3q

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2d3q"
Personal tools