3vec - Revision history

OCA at 10:27, 13 August 2026

2026-08-13T10:27:23Z

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 == Function ==
 [https://www.uniprot.org/uniprot/Q0SE24_RHOJR Q0SE24_RHOJR]
 __TOC__
 </StructureSection>

OCA at 14:26, 14 March 2024

2024-03-14T14:26:03Z

← Older revision		Revision as of 14:26, 14 March 2024
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	<StructureSection load='3vec' size='340' side='right'caption='[[3vec]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3vec' size='340' side='right'caption='[[3vec]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vec]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Rhojr Rhojr~~]. 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>		<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>
	</td></tr><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>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.6Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3ved\|3ved]], [[3vee\|3vee]], [[3vef\|3vef]], [[3veg\|3veg]]~~</~~div~~><~~/td~~></tr>		<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>
	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></~~td><td class="sblockDat"~~>~~dypB, RHA1_ro02407 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=101510 RHOJR])~~</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=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>		<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>		</table>
	~~<div style="background-color:#fffaf0;">~~		== Function ==
	== ~~Publication Abstract from PubMed~~ ==		[https://www.uniprot.org/uniprot/Q0SE24_RHOJR Q0SE24_RHOJR]
	~~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.

	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®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 3vec" style="background-color:#fffaf0;"><~~/~~div>~~
	~~== References ==~~
	~~<references~~/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Rhojr~~]]		[[Category: Rhodococcus jostii RHA1]]
	[[Category: Armstrong, Z]]		[[Category: Armstrong Z]]
	[[Category: Eltis~~, L D~~]]		[[Category: Eltis LD]]
	[[Category: Grigg~~, J C~~]]		[[Category: Grigg JC]]
	[[Category: Murphy~~, M E.P~~]]		[[Category: Murphy MEP]]
	[[Category: Singh, R]]		[[Category: Singh R]]
	~~[[Category: Dyp]]~~
	~~[[Category: Lignan]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Peroxidase~~]]

OCA at 18:40, 27 July 2022

2022-07-27T18:40:58Z

← Older revision		Revision as of 18:40, 27 July 2022
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	==Rhodococcus jostii RHA1 DypB D153A variant in complex with heme==		==Rhodococcus jostii RHA1 DypB D153A variant in complex with heme==
	<StructureSection load='3vec' size='340' side='right' caption='[[3vec]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3vec' size='340' side='right'caption='[[3vec]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vec]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Rhojr Rhojr]. 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 [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VEC FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vec]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhojr Rhojr]. 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>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>		</td></tr><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>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ved\|3ved]], [[3vee\|3vee]], [[3vef\|3vef]], [[3veg\|3veg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ved\|3ved]], [[3vee\|3vee]], [[3vef\|3vef]], [[3veg\|3veg]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dypB, RHA1_ro02407 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=101510 RHOJR])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dypB, RHA1_ro02407 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=101510 RHOJR])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vec OCA], [~~http~~://pdbe.org/3vec PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vec RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vec PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vec 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=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>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Rhojr]]		[[Category: Rhojr]]
	[[Category: Armstrong, Z]]		[[Category: Armstrong, Z]]

OCA at 10:15, 8 November 2017

2017-11-08T10:15:08Z

← Older revision		Revision as of 10:15, 8 November 2017
Line 3:		Line 3:
	<StructureSection load='3vec' size='340' side='right' caption='[[3vec]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3vec' size='340' side='right' caption='[[3vec]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3vec]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Rhosr Rhosr~~]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VEC FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vec]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhojr Rhojr]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VEC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ved\|3ved]], [[3vee\|3vee]], [[3vef\|3vef]], [[3veg\|3veg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ved\|3ved]], [[3vee\|3vee]], [[3vef\|3vef]], [[3veg\|3veg]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dypB, RHA1_ro02407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=101510 ~~RHOSR~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dypB, RHA1_ro02407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=101510 RHOJR])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vec OCA], [http://pdbe.org/3vec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vec RCSB], [http://www.ebi.ac.uk/pdbsum/3vec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vec ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vec OCA], [http://pdbe.org/3vec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vec RCSB], [http://www.ebi.ac.uk/pdbsum/3vec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vec ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Rhosr~~]]		[[Category: Rhojr]]
	[[Category: Armstrong, Z]]		[[Category: Armstrong, Z]]
	[[Category: Eltis, L D]]		[[Category: Eltis, L D]]

OCA at 09:27, 11 August 2016

2016-08-11T09:27:36Z

← Older revision		Revision as of 09:27, 11 August 2016
Line 1:		Line 1:

	==Rhodococcus jostii RHA1 DypB D153A variant in complex with heme==		==Rhodococcus jostii RHA1 DypB D153A variant in complex with heme==
	<StructureSection load='3vec' size='340' side='right' caption='[[3vec]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3vec' size='340' side='right' caption='[[3vec]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VEC FirstGlance]. <br>		<table><tr><td colspan='2'>[[3vec]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhosr Rhosr]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VEC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ved\|3ved]], [[3vee\|3vee]], [[3vef\|3vef]], [[3veg\|3veg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ved\|3ved]], [[3vee\|3vee]], [[3vef\|3vef]], [[3veg\|3veg]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dypB, RHA1_ro02407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~132919 Rhodococcus jostii~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dypB, RHA1_ro02407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=101510 RHOSR])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vec OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vec RCSB], [http://www.ebi.ac.uk/pdbsum/3vec PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vec OCA], [http://pdbe.org/3vec PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vec RCSB], [http://www.ebi.ac.uk/pdbsum/3vec PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vec ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 3vec" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Rhodococcus jostii~~]]		[[Category: Rhosr]]
	[[Category: Armstrong, Z]]		[[Category: Armstrong, Z]]
	[[Category: Eltis, L D]]		[[Category: Eltis, L D]]

OCA at 09:45, 4 January 2015

2015-01-04T09:45:45Z

← Older revision		Revision as of 09:45, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VEC FirstGlance]. <br>		<table><tr><td colspan='2'>[[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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VEC FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ved\|3ved]], [[3vee\|3vee]], [[3vef\|3vef]], [[3veg\|3veg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ved\|3ved]], [[3vee\|3vee]], [[3vef\|3vef]], [[3veg\|3veg]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dypB, RHA1_ro02407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=132919 Rhodococcus jostii])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dypB, RHA1_ro02407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=132919 Rhodococcus jostii])</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vec OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vec RCSB], [http://www.ebi.ac.uk/pdbsum/3vec PDBsum]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vec OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vec RCSB], [http://www.ebi.ac.uk/pdbsum/3vec PDBsum]</span></td></tr>
	<table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Rhodococcus jostii]]		[[Category: Rhodococcus jostii]]
	[[Category: Armstrong, Z.]]		[[Category: Armstrong, Z]]
	[[Category: Eltis, L D.]]		[[Category: Eltis, L D]]
	[[Category: Grigg, J C.]]		[[Category: Grigg, J C]]
	[[Category: Murphy, M E.P.]]		[[Category: Murphy, M E.P]]
	[[Category: Singh, R.]]		[[Category: Singh, R]]
	[[Category: Dyp]]		[[Category: Dyp]]
	[[Category: Lignan]]		[[Category: Lignan]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]

OCA at 09:09, 11 June 2014

2014-06-11T09:09:53Z

← Older revision		Revision as of 09:09, 11 June 2014
Line 1:		Line 1:
	[[~~Image~~:~~3vec~~.~~png~~\|~~left~~\|~~200px~~]]		==Rhodococcus jostii RHA1 DypB D153A variant in complex with heme==
			<StructureSection load='3vec' size='340' side='right' caption='[[3vec]], [[Resolution\|resolution]] 2.60Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[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]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VEC FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ved\|3ved]], [[3vee\|3vee]], [[3vef\|3vef]], [[3veg\|3veg]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dypB, RHA1_ro02407 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=132919 Rhodococcus jostii])</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3vec FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vec OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vec RCSB], [http://www.ebi.ac.uk/pdbsum/3vec PDBsum]</span></td></tr>
			<table>
			<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.

	~~{{STRUCTURE_3vec\| PDB=3vec \| SCENE= }}~~		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>

	~~===Rhodococcus jostii RHA1 DypB D153A variant in complex with heme===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_22308037}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[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].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:022308037<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Rhodococcus jostii]]		[[Category: Rhodococcus jostii]]
	[[Category: Armstrong, Z.]]		[[Category: Armstrong, Z.]]

OCA at 05:06, 29 August 2012

2012-08-29T05:06:10Z

← Older revision		Revision as of 05:06, 29 August 2012
Line 1:		Line 1:
	[[Image:3vec.~~jpg~~\|left\|200px]]		[[Image:3vec.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3vec", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_3vec\| PDB=3vec \| SCENE= }}		{{STRUCTURE_3vec\| PDB=3vec \| SCENE= }}

	===Rhodococcus jostii RHA1 DypB D153A variant in complex with heme===		===Rhodococcus jostii RHA1 DypB D153A variant in complex with heme===

			{{ABSTRACT_PUBMED_22308037}}

	==About this Structure==		==About this Structure==
	[[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].		[[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].

			==Reference==
			<ref group="xtra">PMID:022308037</ref><references group="xtra"/>
	[[Category: Rhodococcus jostii]]		[[Category: Rhodococcus jostii]]
	[[Category: Armstrong, Z.]]		[[Category: Armstrong, Z.]]

OCA: Protected "3vec" [edit=sysop:move=sysop]

2012-01-18T10:56:12Z

Protected "3vec" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:56, 18 January 2012
(No difference)