4jac - Revision history

OCA at 12:02, 1 March 2024

OCA — Fri, 01 Mar 2024 12:02:42 GMT

←Older revision		Revision as of 12:02, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4jac]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JAC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JAC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4jac]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JAC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JAC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.934Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4jac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jac OCA], [https://pdbe.org/4jac PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jac RCSB], [https://www.ebi.ac.uk/pdbsum/4jac PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jac 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=4jac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jac OCA], [https://pdbe.org/4jac PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jac RCSB], [https://www.ebi.ac.uk/pdbsum/4jac PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jac ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q9NAV8_9ANNE Q9NAV8_9ANNE]		[https://www.uniprot.org/uniprot/Q9NAV8_9ANNE Q9NAV8_9ANNE]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The activation of dehaloperoxidase-hemoglobin (DHP) to form a ferryl intermediate requires the distal histidine, H55, to act as an acid base catalyst. The lack of ancillary amino acids in the distal pocket to assist in this process makes H55 even more important to the formation of active intermediates than in conventional peroxidases. Therefore, one can infer that the precise conformation H55 may greatly affect the enzymatic activity. Using site-direct mutagenesis at position T56, immediately adjacent to H55, we have confirmed that subtle changes in the conformation of H55 affect the catalytic efficiency of DHP. Mutating T56 to a smaller amino acid appears to permit H55 to rotate with relatively low barriers between conformations in the distal pocket, which may lead to an increase in catalytic activity. On the other hand, larger amino acids in the neighboring site appear to restrict the rotation of H55 due to the steric hindrance. In the case of T56V, which is an isosteric mutation, H55 appears less mobile, but forced to be closer to the heme iron than in wild type. Both proximity to the heme iron and flexibility of motion in some of the mutants can result in an increased catalytic rate, but can also lead to protein inactivation due to ligation of H55 to the heme iron, which is known as hemichrome formation. A balance of enzymatic rate and protein stability with respect to hemichrome formation appears to be optimum in wild type DHP (WT-DHP).
-
-	The role of T56 in controlling the flexibility of the distal histidine in dehaloperoxidase-hemoglobin from Amphitrite ornata.,Jiang S, Wright I, Swartz P, Franzen S Biochim Biophys Acta. 2013 Oct;1834(10):2020-9. doi:, 10.1016/j.bbapap.2013.06.005. Epub 2013 Jun 20. PMID:23792762<ref>PMID:23792762</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4jac" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Dehaloperoxidase 3D structures\|Dehaloperoxidase 3D structures]]		*[[Dehaloperoxidase 3D structures\|Dehaloperoxidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:02, 24 November 2022

OCA — Thu, 24 Nov 2022 11:02:11 GMT

←Older revision		Revision as of 11:02, 24 November 2022
Line 3:		Line 3:
	<StructureSection load='4jac' size='340' side='right'caption='[[4jac]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='4jac' size='340' side='right'caption='[[4jac]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4jac]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JAC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4JAC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4jac]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JAC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4JAC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4jac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jac OCA], [~~http~~://pdbe.org/4jac PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4jac RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4jac PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4jac 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=4jac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jac OCA], [https://pdbe.org/4jac PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4jac RCSB], [https://www.ebi.ac.uk/pdbsum/4jac PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4jac ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9NAV8_9ANNE Q9NAV8_9ANNE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 20:

	==See Also==		==See Also==
-	*[[Dehaloperoxidase\|Dehaloperoxidase]]	+	*[[Dehaloperoxidase 3D structures\|Dehaloperoxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 27:
	[[Category: Amphitrite ornata]]		[[Category: Amphitrite ornata]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Franzen, S]]	+	[[Category: Franzen S]]
-	[[Category: Swartz~~, P D]]~~	+	[[Category: Swartz PD]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Peroxidase~~]]	+

OCA at 09:21, 3 April 2019

OCA — Wed, 03 Apr 2019 09:21:54 GMT

←Older revision		Revision as of 09:21, 3 April 2019
Line 1:		Line 1:

	==Dehaloperoxidase-Hemoglobin T56S==		==Dehaloperoxidase-Hemoglobin T56S==
-	<StructureSection load='4jac' size='340' side='right' caption='[[4jac]], [[Resolution\|resolution]] 1.93Å' scene=''>	+	<StructureSection load='4jac' size='340' side='right'caption='[[4jac]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4jac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JAC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4jac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JAC FirstGlance]. <br>
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Amphitrite ornata]]		[[Category: Amphitrite ornata]]
		+	[[Category: Large Structures]]
	[[Category: Franzen, S]]		[[Category: Franzen, S]]
	[[Category: Swartz, P D]]		[[Category: Swartz, P D]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]

OCA at 02:03, 5 August 2016

OCA — Fri, 05 Aug 2016 02:03:41 GMT

←Older revision		Revision as of 02:03, 5 August 2016
Line 1:		Line 1:
		+
	==Dehaloperoxidase-Hemoglobin T56S==		==Dehaloperoxidase-Hemoglobin T56S==
	<StructureSection load='4jac' size='340' side='right' caption='[[4jac]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='4jac' size='340' side='right' caption='[[4jac]], [[Resolution\|resolution]] 1.93Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4jac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JAC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4jac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JAC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4jac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jac OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jac RCSB], [http://www.ebi.ac.uk/pdbsum/4jac 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=4jac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jac OCA], [http://pdbe.org/4jac PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4jac RCSB], [http://www.ebi.ac.uk/pdbsum/4jac PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4jac ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 4jac" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 18:32, 21 December 2014

OCA — Sun, 21 Dec 2014 18:32:30 GMT

←Older revision		Revision as of 18:32, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4jac~~\| ~~PDB~~=4jac \| ~~SCENE~~= }}	+	==Dehaloperoxidase-Hemoglobin T56S==
-	===~~Dehaloperoxidase~~-~~Hemoglobin T56S~~===	+	<StructureSection load='4jac' size='340' side='right' caption='[[4jac]], [[Resolution\|resolution]] 1.93Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23792762}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4jac]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Amphitrite_ornata Amphitrite ornata]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JAC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4JAC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4jac FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4jac OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4jac RCSB], [http://www.ebi.ac.uk/pdbsum/4jac PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The activation of dehaloperoxidase-hemoglobin (DHP) to form a ferryl intermediate requires the distal histidine, H55, to act as an acid base catalyst. The lack of ancillary amino acids in the distal pocket to assist in this process makes H55 even more important to the formation of active intermediates than in conventional peroxidases. Therefore, one can infer that the precise conformation H55 may greatly affect the enzymatic activity. Using site-direct mutagenesis at position T56, immediately adjacent to H55, we have confirmed that subtle changes in the conformation of H55 affect the catalytic efficiency of DHP. Mutating T56 to a smaller amino acid appears to permit H55 to rotate with relatively low barriers between conformations in the distal pocket, which may lead to an increase in catalytic activity. On the other hand, larger amino acids in the neighboring site appear to restrict the rotation of H55 due to the steric hindrance. In the case of T56V, which is an isosteric mutation, H55 appears less mobile, but forced to be closer to the heme iron than in wild type. Both proximity to the heme iron and flexibility of motion in some of the mutants can result in an increased catalytic rate, but can also lead to protein inactivation due to ligation of H55 to the heme iron, which is known as hemichrome formation. A balance of enzymatic rate and protein stability with respect to hemichrome formation appears to be optimum in wild type DHP (WT-DHP).

-	~~==About this Structure==~~	+	The role of T56 in controlling the flexibility of the distal histidine in dehaloperoxidase-hemoglobin from Amphitrite ornata.,Jiang S, Wright I, Swartz P, Franzen S Biochim Biophys Acta. 2013 Oct;1834(10):2020-9. doi:, 10.1016/j.bbapap.2013.06.005. Epub 2013 Jun 20. PMID:23792762<ref>PMID:23792762</ref>
-	~~[[4jac]] is a 2 chain structure. Full crystallographic information is available~~ from ~~[http~~:/~~/oca~~.~~weizmann~~.ac.~~il/oca-bin/ocashort?id=4JAC OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:023792762</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
-	[[Category: Franzen, S.]]	+
-	[[Category: Swartz, P D.]]	+	==See Also==
		+	*[[Dehaloperoxidase\|Dehaloperoxidase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Amphitrite ornata]]
		+	[[Category: Franzen, S]]
		+	[[Category: Swartz, P D]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]

OCA at 10:23, 27 November 2013

OCA — Wed, 27 Nov 2013 10:23:22 GMT

←Older revision		Revision as of 10:23, 27 November 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4jac\| PDB=4jac \| SCENE= }}
		+	===Dehaloperoxidase-Hemoglobin T56S===
		+	{{ABSTRACT_PUBMED_23792762}}

-	~~The entry~~ 4jac is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
		+	[[4jac]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4JAC OCA].

-	~~Authors~~: Franzen, S., Swartz, P.D.	+	==Reference==
-		+	<ref group="xtra">PMID:023792762</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Dehaloperoxidase-Hemoglobin T56S~~	+	[[Category: Franzen, S.]]
		+	[[Category: Swartz, P D.]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Peroxidase]]

OCA at 13:51, 6 March 2013

OCA — Wed, 06 Mar 2013 13:51:07 GMT

←Older revision		Revision as of 13:51, 6 March 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4jac is ON HOLD	+	The entry 4jac is ON HOLD until Paper Publication

-	Authors: Franzen, ~~Stefan~~, Swartz, ~~Paul~~ D.	+	Authors: Franzen, S., Swartz, P.D.

	Description: Dehaloperoxidase-Hemoglobin T56S		Description: Dehaloperoxidase-Hemoglobin T56S

OCA: Protected "4jac" [edit=sysop:move=sysop]

OCA — Wed, 27 Feb 2013 14:27:10 GMT

Protected "4jac" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:27, 27 February 2013

OCA: New page: '''Unreleased structure''' The entry 4jac is ON HOLD Authors: Franzen, Stefan, Swartz, Paul D. Description: Dehaloperoxidase-Hemoglobin T56S

OCA — Wed, 27 Feb 2013 14:27:08 GMT

New page: '''Unreleased structure''' The entry 4jac is ON HOLD Authors: Franzen, Stefan, Swartz, Paul D. Description: Dehaloperoxidase-Hemoglobin T56S

New page

'''Unreleased structure'''

The entry 4jac is ON HOLD

Authors: Franzen, Stefan, Swartz, Paul D.

Description: Dehaloperoxidase-Hemoglobin T56S