3vec: Difference between revisions

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==Rhodococcus jostii RHA1 DypB D153A variant in complex with heme==
The line below this paragraph, containing "STRUCTURE_3vec", creates the "Structure Box" on the page.
<StructureSection load='3vec' size='340' side='right'caption='[[3vec]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[3vec]] is a 3 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=3VEC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VEC FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
{{STRUCTURE_3vec|  PDB=3vec  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vec OCA], [https://pdbe.org/3vec PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vec RCSB], [https://www.ebi.ac.uk/pdbsum/3vec PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vec ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q0SE24_RHOJR Q0SE24_RHOJR]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DypB from Rhodococcus jostii RHA1 is a bacterial dye-decolorizing peroxidase (DyP) that oxidizes lignin and Mn(II). Three residues interact with the iron-bound solvent species in ferric DypB: Asn-246 and the conserved Asp-153 and Arg-244. Substitution of either Asp-153 or Asn-246 with alanine minimally affected the second order rate constant for Compound I formation (k(1) approximately 10(5) M(-1)s(-1)) and the specificity constant (k(cat)/K(m)) for H(2)O(2). Even in the D153A/N246A double variant, these values were reduced less than 30-fold. However, these substitutions dramatically reduced the stability of Compound I (t(1/2) approximately 0.13 s) as compared with the wild-type enzyme (540 s). By contrast, substitution of Arg-244 with leucine abolished the peroxidase activity, and heme iron of the variant showed a pH-dependent transition from high spin (pH 5) to low spin (pH 8.5). Two variants were designed to mimic the plant peroxidase active site: D153H, which was more than an order of magnitude less reactive with H(2)O(2), and N246H, which had no detectable peroxidase activity. X-ray crystallographic studies revealed that structural changes in the variants are confined to the distal heme environment. The data establish an essential role for Arg-244 in Compound I formation in DypB, possibly through charge stabilization and proton transfer. The principle roles of Asp-153 and Asn-246 appear to be in modulating the subsequent reactivity of Compound I. These results expand the range of residues known to catalyze Compound I formation in heme peroxidases.


===Rhodococcus jostii RHA1 DypB D153A variant in complex with heme===
Distal heme pocket residues of B-type dye-decolorizing peroxidase: arginine but not aspartate is essential for peroxidase activity.,Singh R, Grigg JC, Armstrong Z, Murphy ME, Eltis LD J Biol Chem. 2012 Mar 23;287(13):10623-30. Epub 2012 Feb 3. PMID:22308037<ref>PMID:22308037</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==About this Structure==
</div>
[[3vec]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodococcus_jostii Rhodococcus jostii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VEC OCA].
<div class="pdbe-citations 3vec" style="background-color:#fffaf0;"></div>
[[Category: Rhodococcus jostii]]
== References ==
[[Category: Armstrong, Z.]]
<references/>
[[Category: Eltis, L D.]]
__TOC__
[[Category: Grigg, J C.]]
</StructureSection>
[[Category: Murphy, M E.P.]]
[[Category: Large Structures]]
[[Category: Singh, R.]]
[[Category: Rhodococcus jostii RHA1]]
[[Category: Dyp]]
[[Category: Armstrong Z]]
[[Category: Lignan]]
[[Category: Eltis LD]]
[[Category: Oxidoreductase]]
[[Category: Grigg JC]]
[[Category: Peroxidase]]
[[Category: Murphy MEP]]
[[Category: Singh R]]
Retrieved from "https://proteopedia.org/3vec"