5v5r - Revision history

OCA at 13:42, 4 October 2023

OCA — Wed, 04 Oct 2023 13:42:12 GMT

←Older revision		Revision as of 13:42, 4 October 2023
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	<StructureSection load='5v5r' size='340' side='right'caption='[[5v5r]], [[Resolution\|resolution]] 1.20Å' scene=''>		<StructureSection load='5v5r' size='340' side='right'caption='[[5v5r]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v5r]] 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=5V5R OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V5R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v5r]] 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=5V5R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V5R FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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]] 1.2Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v5j\|5v5j]], [[5v5q\|5v5q]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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=5v5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v5r OCA], [~~http~~://pdbe.org/5v5r PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v5r RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v5r PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v5r 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=5v5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v5r OCA], [https://pdbe.org/5v5r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v5r RCSB], [https://www.ebi.ac.uk/pdbsum/5v5r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v5r 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 ==
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	[[Category: Amphitrite ornata]]		[[Category: Amphitrite ornata]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Carey~~, L M~~]]	+	[[Category: Carey LM]]
-	[[Category: Ghiladi~~, R A]]~~	+	[[Category: Ghiladi RA]]
-	~~[[Category: Globin]]~~	+
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Oxygen transport]]~~	+
-	~~[[Category: Peroxidase]]~~	+
-	~~[[Category: Peroxygenase~~]]	+

OCA at 08:02, 27 November 2019

OCA — Wed, 27 Nov 2019 08:02:33 GMT

←Older revision		Revision as of 08:02, 27 November 2019
Line 19:		Line 19:

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

OCA at 08:03, 3 April 2019

OCA — Wed, 03 Apr 2019 08:03:25 GMT

←Older revision		Revision as of 08:03, 3 April 2019
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	==Dehaloperoxidase A I9L mutant==		==Dehaloperoxidase A I9L mutant==
-	<StructureSection load='5v5r' size='340' side='right' caption='[[5v5r]], [[Resolution\|resolution]] 1.20Å' scene=''>	+	<StructureSection load='5v5r' size='340' side='right'caption='[[5v5r]], [[Resolution\|resolution]] 1.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v5r]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V5R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V5R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v5r]] 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=5V5R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V5R FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v5j\|5v5j]], [[5v5q\|5v5q]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v5j\|5v5j]], [[5v5q\|5v5q]]</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=5v5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v5r OCA], [http://pdbe.org/5v5r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v5r RCSB], [http://www.ebi.ac.uk/pdbsum/5v5r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v5r 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=5v5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v5r OCA], [http://pdbe.org/5v5r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v5r RCSB], [http://www.ebi.ac.uk/pdbsum/5v5r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v5r ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The coelomic hemoglobin of Amphitrite ornata, termed dehaloperoxidase (DHP), is the first known multifunctional catalytic globin to possess biologically-relevant peroxidase and peroxygenase activities. Although the two isoenzymes of DHP, A and B, differ in sequence by only 5 amino acids out of 137 residues, DHP B consistently exhibits a greater activity than isoenzyme A. To delineate the contributions of each amino acid substitution to the activity of either isoenzyme, the substitutions of the five amino acids were systematically investigated, individually and in combination, using 22 mutants. Biochemical assays and mechanistic studies demonstrated that the mutants that only contained the I9L substitution showed increased i) kcat values (peroxidase activity), ii) 5-Br-indole conversion and binding affinity (peroxygenase activity), and iii) rate of Compound ES formation (enzyme activation). Whereas the X-ray structures of the oxyferrous forms of DHP B (L9I) (1.96A), DHP A (I9L) (1.20A), and WT DHP B (1.81A) showed no significant differences, UV-visible spectroscopy (ASoret/A380 ratio) revealed that the I9L substitution increased the 5-coordinate high-spin heme population characterized by the "open" conformation (i.e., distal histidine swung out of the pocket), which likely favors substrate binding. The positioning of the distal histidine closer to the heme cofactor in the solution state also appears to facilitate activation of DHP via the Compound ES intermediate. Taken together, the studies undertaken here shed light on the structure-function relationship in dehaloperoxidase, but also help to establish the foundation for understanding how enzymatic activity can be tuned in isoenzymes of a multifunctional catalytic globin.
		+
		+	How nature tunes isoenzyme activity in the multifunctional catalytic globin dehaloperoxidase from Amphitrite ornata.,Carey LM, Gavenko R, Svistunenko DA, Ghiladi RA Biochim Biophys Acta Proteins Proteom. 2018 Feb;1866(2):230-241. doi:, 10.1016/j.bbapap.2017.11.004. Epub 2017 Nov 9. PMID:29128676<ref>PMID:29128676</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5v5r" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Dehaloperoxidase\|Dehaloperoxidase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Amphitrite ornata]]
		+	[[Category: Large Structures]]
	[[Category: Carey, L M]]		[[Category: Carey, L M]]
	[[Category: Ghiladi, R A]]		[[Category: Ghiladi, R A]]

OCA at 07:32, 21 March 2018

OCA — Wed, 21 Mar 2018 07:32:19 GMT

←Older revision		Revision as of 07:32, 21 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5v5r is ~~ON HOLD until Paper Publication~~	+	==Dehaloperoxidase A I9L mutant==
-		+	<StructureSection load='5v5r' size='340' side='right' caption='[[5v5r]], [[Resolution\|resolution]] 1.20Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5v5r]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V5R OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V5R FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v5j\|5v5j]], [[5v5q\|5v5q]]</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=5v5r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v5r OCA], [http://pdbe.org/5v5r PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v5r RCSB], [http://www.ebi.ac.uk/pdbsum/5v5r PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v5r ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carey, L M]]
		+	[[Category: Ghiladi, R A]]
		+	[[Category: Globin]]
		+	[[Category: Mutant]]
		+	[[Category: Oxygen transport]]
		+	[[Category: Peroxidase]]
		+	[[Category: Peroxygenase]]

OCA at 12:00, 27 April 2017

OCA — Thu, 27 Apr 2017 12:00:51 GMT

←Older revision		Revision as of 12:00, 27 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5v5r is ON HOLD	+	The entry 5v5r is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5v5r" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 11:38:07 GMT

Protected "5v5r" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:38, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5v5r is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Apr 2017 11:38:06 GMT

New page: '''Unreleased structure''' The entry 5v5r is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5v5r is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]