5amm - Revision history

OCA at 11:13, 10 January 2024

OCA — Wed, 10 Jan 2024 11:13:30 GMT

←Older revision		Revision as of 11:13, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5amm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AMM FirstGlance]. <br>		<table><tr><td colspan='2'>[[5amm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AMM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 2.09Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=5amm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amm OCA], [https://pdbe.org/5amm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5amm RCSB], [https://www.ebi.ac.uk/pdbsum/5amm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5amm 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=5amm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amm OCA], [https://pdbe.org/5amm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5amm RCSB], [https://www.ebi.ac.uk/pdbsum/5amm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5amm ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:15, 31 May 2023

OCA — Wed, 31 May 2023 06:15:21 GMT

←Older revision		Revision as of 06:15, 31 May 2023
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	<StructureSection load='5amm' size='340' side='right'caption='[[5amm]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='5amm' size='340' side='right'caption='[[5amm]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5amm]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Leima Leima~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5AMM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5amm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AMM FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5al9\|5al9]], [[5ala\|5ala]]~~</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=5amm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amm OCA], [https://pdbe.org/5amm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5amm RCSB], [https://www.ebi.ac.uk/pdbsum/5amm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5amm 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=5amm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amm OCA], [~~http~~://pdbe.org/5amm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5amm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5amm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5amm ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q4Q3K2_LEIMA Q4Q3K2_LEIMA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Leima~~]]	+	[[Category: Leishmania major]]
-	[[Category: Arce~~, A P~~]]	+	[[Category: Arce AP]]
-	[[Category: Chreifi, G]]	+	[[Category: Chreifi G]]
-	[[Category: Fields~~, J B~~]]	+	[[Category: Fields JB]]
-	[[Category: Heyden, M]]	+	[[Category: Heyden M]]
-	[[Category: Hollingsworth~~, S A~~]]	+	[[Category: Hollingsworth SA]]
-	[[Category: Magana-Garcia~~, H I~~]]	+	[[Category: Magana-Garcia HI]]
-	[[Category: Poulos~~, T L~~]]	+	[[Category: Poulos TL]]
-	[[Category: Tobias~~, D J]]~~	+	[[Category: Tobias DJ]]
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 07:18, 3 July 2019

OCA — Wed, 03 Jul 2019 07:18:29 GMT

←Older revision		Revision as of 07:18, 3 July 2019
Line 1:		Line 1:
		+
	==Structure of Leishmania major peroxidase D211N mutant==		==Structure of Leishmania major peroxidase D211N mutant==
-	<StructureSection load='5amm' size='340' side='right' caption='[[5amm]], [[Resolution\|resolution]] 2.09Å' scene=''>	+	<StructureSection load='5amm' size='340' side='right'caption='[[5amm]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5amm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AMM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5amm]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Leima Leima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AMM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5al9\|5al9]], [[5ala\|5ala]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5al9\|5al9]], [[5ala\|5ala]]</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=5amm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amm OCA], [http://pdbe.org/5amm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5amm RCSB], [http://www.ebi.ac.uk/pdbsum/5amm 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=5amm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amm OCA], [http://pdbe.org/5amm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5amm RCSB], [http://www.ebi.ac.uk/pdbsum/5amm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5amm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5amm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5amm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ascorbate peroxidase 3D structures\|Ascorbate peroxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Leima]]
	[[Category: Arce, A P]]		[[Category: Arce, A P]]
	[[Category: Chreifi, G]]		[[Category: Chreifi, G]]

OCA at 13:43, 9 December 2015

OCA — Wed, 09 Dec 2015 13:43:35 GMT

←Older revision		Revision as of 13:43, 9 December 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure of Leishmania major peroxidase D211N mutant==
		+	<StructureSection load='5amm' size='340' side='right' caption='[[5amm]], [[Resolution\|resolution]] 2.09Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5amm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AMM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5AMM FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5al9\|5al9]], [[5ala\|5ala]]</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=5amm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5amm OCA], [http://pdbe.org/5amm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5amm RCSB], [http://www.ebi.ac.uk/pdbsum/5amm PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Leishmania major, the parasitic causative agent of leishmaniasis, produces a heme peroxidase (LmP), which catalyzes the peroxidation of mitochondrial cytochrome c (LmCytc) for protection from reactive oxygen species produced by the host. The association of LmP and LmCytc, which is known from kinetics measurements to be very fast ( approximately 108 M-1 s-1), does not involve major conformational changes and has been suggested to be dominated by electrostatic interactions. We used Brownian dynamics simulations to investigate the mechanism of formation of the LmP-LmCytc complex. Our simulations confirm the importance of electrostatic interactions involving the negatively charged D211 residue at the LmP active site, and reveal a previously unrecognized role in complex formation for negatively charged residues in helix A of LmP. The crystal structure of the D211N mutant of LmP reported herein is essentially identical to that of wild-type LmP, reinforcing the notion that it is the loss of charge at the active site, and not a change in structure, that reduces the association rate of the D211N variant of LmP. The Brownian dynamics simulations further show that complex formation occurs via a "bind and crawl" mechanism, in which LmCytc first docks to a location on helix A that is far from the active site, forming an initial encounter complex, and then moves along helix A to the active site. An atomistic molecular dynamics simulation confirms the helix A binding site, and steady state activity assays and stopped-flow kinetics measurements confirm the role of helix A charges in the association mechanism.

-	~~The entry 5amm is ON HOLD until Paper Publication~~	+	"Bind and Crawl" Association Mechanism of Leishmania major Peroxidase and Cytochrome c Revealed by Brownian and Molecular Dynamics Simulations.,Fields JB, Hollingsworth SA, Chreifi G, Heyden M, Arce AP, Magana-Garcia HI, Poulos TL, Tobias DJ Biochemistry. 2015 Dec 3. PMID:26598276<ref>PMID:26598276</ref>

-	~~Authors: Chreifi~~, G.~~, Fields, J.B., Hollingsworth,~~ S.~~A., Heyden, M., Arce, A.P., Magana-Garcia, H.I., Poulos, T.L., Tobias, D.J~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Structure of Leishmania major peroxidase D211N mutant~~	+	<div class="pdbe-citations 5amm" style="background-color:#fffaf0;"></div>
-	~~[[Category: Unreleased Structures]]~~	+	== References ==
-	[[Category: ~~Magana-Garcia~~, ~~H.I~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arce, A P]]
	[[Category: Chreifi, G]]		[[Category: Chreifi, G]]
-	~~[[Category: Arce, A.P]]~~	+	[[Category: Fields, J B]]
-	~~[[Category: Poulos, T.L]]~~	+
-	[[Category: Fields, J.B]]	+
-	~~[[Category: Tobias, D.J~~]]	+
	[[Category: Heyden, M]]		[[Category: Heyden, M]]
-	[[Category: Hollingsworth, S.A]]	+	[[Category: Hollingsworth, S A]]
		+	[[Category: Magana-Garcia, H I]]
		+	[[Category: Poulos, T L]]
		+	[[Category: Tobias, D J]]
		+	[[Category: Oxidoreductase]]

OCA at 11:29, 13 May 2015

OCA — Wed, 13 May 2015 11:29:15 GMT

←Older revision		Revision as of 11:29, 13 May 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Chreifi, G., Fields, J.B., Hollingsworth, S.A., Heyden, M., Arce, A.P., Magana-Garcia, H.I., Poulos, T.L., Tobias, D.J.		Authors: Chreifi, G., Fields, J.B., Hollingsworth, S.A., Heyden, M., Arce, A.P., Magana-Garcia, H.I., Poulos, T.L., Tobias, D.J.

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

OCA — Wed, 18 Mar 2015 11:15:11 GMT

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

←Older revision

Revision as of 11:15, 18 March 2015

OCA: New page: '''Unreleased structure''' The entry 5amm is ON HOLD Authors: Chreifi, G., Fields, J.B., Hollingsworth, S.A., Heyden, M., Arce, A.P., Magana-Garcia, H.I., Poulos, T.L., Tobias, D.J. De...

OCA — Wed, 18 Mar 2015 11:15:10 GMT

New page: '''Unreleased structure''' The entry 5amm is ON HOLD Authors: Chreifi, G., Fields, J.B., Hollingsworth, S.A., Heyden, M., Arce, A.P., Magana-Garcia, H.I., Poulos, T.L., Tobias, D.J. De...

New page

'''Unreleased structure'''

The entry 5amm is ON HOLD

Authors: Chreifi, G., Fields, J.B., Hollingsworth, S.A., Heyden, M., Arce, A.P., Magana-Garcia, H.I., Poulos, T.L., Tobias, D.J.

Description: Structure of Leishmania major peroxidase D211N mutant
[[Category: Unreleased Structures]]
[[Category: Magana-Garcia, H.I]]
[[Category: Chreifi, G]]
[[Category: Arce, A.P]]
[[Category: Poulos, T.L]]
[[Category: Fields, J.B]]
[[Category: Tobias, D.J]]
[[Category: Heyden, M]]
[[Category: Hollingsworth, S.A]]