1me5 - Revision history

OCA at 07:43, 14 February 2024

OCA — Wed, 14 Feb 2024 07:43:24 GMT

←Older revision		Revision as of 07:43, 14 February 2024
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	<StructureSection load='1me5' size='340' side='right'caption='[[1me5]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1me5' size='340' side='right'caption='[[1me5]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus~~ tuberculosis~~" (zopf 1883) klein 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~<div style='overflow: auto; max~~-~~height: 3em;'>~~[[~~1lw1~~\|~~1lw1~~]]~~</div>~~</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]] 2.4Å</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=1me5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me5 OCA], [https://pdbe.org/1me5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1me5 RCSB], [https://www.ebi.ac.uk/pdbsum/1me5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1me5 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=1me5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me5 OCA], [https://pdbe.org/1me5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1me5 RCSB], [https://www.ebi.ac.uk/pdbsum/1me5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1me5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AHPD_MYCTU AHPD_MYCTU]] Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity.<ref>PMID:10766746</ref> <ref>PMID:11799204</ref> <ref>PMID:12761216</ref> Together with AhpC, DlaT and Lpd, constitutes an NADH-dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system.<ref>PMID:10766746</ref> <ref>PMID:11799204</ref> <ref>PMID:12761216</ref>	+	[https://www.uniprot.org/uniprot/AHPD_MYCTU AHPD_MYCTU] Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity.<ref>PMID:10766746</ref> <ref>PMID:11799204</ref> <ref>PMID:12761216</ref> Together with AhpC, DlaT and Lpd, constitutes an NADH-dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system.<ref>PMID:10766746</ref> <ref>PMID:11799204</ref> <ref>PMID:12761216</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1me5 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1me5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	AhpD, a protein with two cysteine residues, is required for physiological reduction of the Mycobacterium tuberculosis alkylhydroperoxidase AhpC. AhpD also has an alkylhydroperoxidase activity of its own. The AhpC/AhpD system provides critical antioxidant protection, particularly in the absence of the catalase-peroxidase KatG, which is suppressed in most isoniazid-resistant strains. Based on the crystal structure, we proposed recently a catalytic mechanism for AhpD involving a proton relay in which the Glu118 carboxylate group, via His137 and a water molecule, deprotonates the catalytic residue Cys133 (Nunn, C. M., Djordjevic, S., Hillas, P. J., Nishida, C., and Ortiz de Montellano, P. R. (2002) J. Biol. Chem. 277, 20033-20040). A possible role for His132 in subsequent formation of the Cys133-Cys130 disulfide bond was also noted. To test this proposed mechanism, we have expressed the H137F, H137Q, H132F, H132Q, E118F, E118Q, C133S, and C130S mutants of AhpD, determined the crystal structures of the H137F and H132Q mutants, estimated the pKa values of the cysteine residues, and defined the kinetic properties of the mutant proteins. The collective results strongly support the proposed catalytic mechanism for AhpD.
-
-	The mechanism of Mycobacterium tuberculosis alkylhydroperoxidase AhpD as defined by mutagenesis, crystallography, and kinetics.,Koshkin A, Nunn CM, Djordjevic S, Ortiz de Montellano PR J Biol Chem. 2003 Aug 8;278(32):29502-8. Epub 2003 May 21. PMID:12761216<ref>PMID:12761216</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1me5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Djordjevic, S~~]]	+	[[Category: Mycobacterium tuberculosis]]
-	[[Category: ~~Montellano, P R.Ortiz de~~]]	+	[[Category: Djordjevic S]]
-	[[Category: Nunn~~, C M~~]]	+	[[Category: Nunn CM]]
-	[[Category: ~~Alpha helical]]~~	+	[[Category: Ortiz de Montellano PR]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Trimer~~]]	+

OCA at 06:51, 25 August 2021

OCA — Wed, 25 Aug 2021 06:51:00 GMT

←Older revision		Revision as of 06:51, 25 August 2021
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	<StructureSection load='1me5' size='340' side='right'caption='[[1me5]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1me5' size='340' side='right'caption='[[1me5]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lw1\|1lw1]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lw1\|1lw1]]</div></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=1me5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me5 OCA], [~~http~~://pdbe.org/1me5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1me5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1me5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1me5 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=1me5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me5 OCA], [https://pdbe.org/1me5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1me5 RCSB], [https://www.ebi.ac.uk/pdbsum/1me5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1me5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AHPD_MYCTU AHPD_MYCTU]] Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity.<ref>PMID:10766746</ref> <ref>PMID:11799204</ref> <ref>PMID:12761216</ref> Together with AhpC, DlaT and Lpd, constitutes an NADH-dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system.<ref>PMID:10766746</ref> <ref>PMID:11799204</ref> <ref>PMID:12761216</ref>	+	[[https://www.uniprot.org/uniprot/AHPD_MYCTU AHPD_MYCTU]] Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity.<ref>PMID:10766746</ref> <ref>PMID:11799204</ref> <ref>PMID:12761216</ref> Together with AhpC, DlaT and Lpd, constitutes an NADH-dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system.<ref>PMID:10766746</ref> <ref>PMID:11799204</ref> <ref>PMID:12761216</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:03, 13 November 2019

OCA — Wed, 13 Nov 2019 12:03:10 GMT

←Older revision		Revision as of 12:03, 13 November 2019
Line 1:		Line 1:

	==Crystal Structure of Mycobacterium Tuberculosis Alkylperoxidase AhpD H132Q Mutant==		==Crystal Structure of Mycobacterium Tuberculosis Alkylperoxidase AhpD H132Q Mutant==
-	<StructureSection load='1me5' size='340' side='right' caption='[[1me5]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1me5' size='340' side='right'caption='[[1me5]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>
Line 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Djordjevic, S]]		[[Category: Djordjevic, S]]
	[[Category: Montellano, P R.Ortiz de]]		[[Category: Montellano, P R.Ortiz de]]

OCA at 06:24, 31 January 2018

OCA — Wed, 31 Jan 2018 06:24:18 GMT

←Older revision		Revision as of 06:24, 31 January 2018
Line 1:		Line 1:
		+
	==Crystal Structure of Mycobacterium Tuberculosis Alkylperoxidase AhpD H132Q Mutant==		==Crystal Structure of Mycobacterium Tuberculosis Alkylperoxidase AhpD H132Q Mutant==
	<StructureSection load='1me5' size='340' side='right' caption='[[1me5]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1me5' size='340' side='right' caption='[[1me5]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lw1\|1lw1]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lw1\|1lw1]]</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=1me5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me5 OCA], [http://pdbe.org/1me5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1me5 RCSB], [http://www.ebi.ac.uk/pdbsum/1me5 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=1me5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me5 OCA], [http://pdbe.org/1me5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1me5 RCSB], [http://www.ebi.ac.uk/pdbsum/1me5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1me5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/me/1me5_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/me/1me5_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 12:35, 9 February 2016

OCA — Tue, 09 Feb 2016 12:35:47 GMT

←Older revision		Revision as of 12:35, 9 February 2016
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1me5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:18, 10 September 2015

OCA — Thu, 10 Sep 2015 22:18:42 GMT

←Older revision		Revision as of 22:18, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1me5' size='340' side='right' caption='[[1me5]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1me5' size='340' side='right' caption='[[1me5]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium~~ tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lw1\|1lw1]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lw1\|1lw1]]</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=1me5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1me5 RCSB], [http://www.ebi.ac.uk/pdbsum/1me5 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=1me5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me5 OCA], [http://pdbe.org/1me5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1me5 RCSB], [http://www.ebi.ac.uk/pdbsum/1me5 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 26:		Line 26:
	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 1me5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Mycobacterium tuberculosis]]
	[[Category: Djordjevic, S]]		[[Category: Djordjevic, S]]
	[[Category: Montellano, P R.Ortiz de]]		[[Category: Montellano, P R.Ortiz de]]

OCA at 06:51, 25 December 2014

OCA — Thu, 25 Dec 2014 06:51:41 GMT

←Older revision		Revision as of 06:51, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lw1\|1lw1]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lw1\|1lw1]]</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=1me5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1me5 RCSB], [http://www.ebi.ac.uk/pdbsum/1me5 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=1me5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1me5 RCSB], [http://www.ebi.ac.uk/pdbsum/1me5 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AHPD_MYCTU AHPD_MYCTU]] Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity.<ref>PMID:10766746</ref> <ref>PMID:11799204</ref> <ref>PMID:12761216</ref> Together with AhpC, DlaT and Lpd, constitutes an NADH-dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system.<ref>PMID:10766746</ref> <ref>PMID:11799204</ref> <ref>PMID:12761216</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 29:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Djordjevic, S.]]	+	[[Category: Djordjevic, S]]
-	[[Category: Montellano, P R.Ortiz de.]]	+	[[Category: Montellano, P R.Ortiz de]]
-	[[Category: Nunn, C M.]]	+	[[Category: Nunn, C M]]
	[[Category: Alpha helical]]		[[Category: Alpha helical]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Trimer]]		[[Category: Trimer]]

OCA at 13:04, 28 September 2014

OCA — Sun, 28 Sep 2014 13:04:41 GMT

←Older revision		Revision as of 13:04, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1me5.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of Mycobacterium Tuberculosis Alkylperoxidase AhpD H132Q Mutant==
		+	<StructureSection load='1me5' size='340' side='right' caption='[[1me5]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1me5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ME5 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lw1\|1lw1]]</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=1me5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1me5 RCSB], [http://www.ebi.ac.uk/pdbsum/1me5 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/me/1me5_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	AhpD, a protein with two cysteine residues, is required for physiological reduction of the Mycobacterium tuberculosis alkylhydroperoxidase AhpC. AhpD also has an alkylhydroperoxidase activity of its own. The AhpC/AhpD system provides critical antioxidant protection, particularly in the absence of the catalase-peroxidase KatG, which is suppressed in most isoniazid-resistant strains. Based on the crystal structure, we proposed recently a catalytic mechanism for AhpD involving a proton relay in which the Glu118 carboxylate group, via His137 and a water molecule, deprotonates the catalytic residue Cys133 (Nunn, C. M., Djordjevic, S., Hillas, P. J., Nishida, C., and Ortiz de Montellano, P. R. (2002) J. Biol. Chem. 277, 20033-20040). A possible role for His132 in subsequent formation of the Cys133-Cys130 disulfide bond was also noted. To test this proposed mechanism, we have expressed the H137F, H137Q, H132F, H132Q, E118F, E118Q, C133S, and C130S mutants of AhpD, determined the crystal structures of the H137F and H132Q mutants, estimated the pKa values of the cysteine residues, and defined the kinetic properties of the mutant proteins. The collective results strongly support the proposed catalytic mechanism for AhpD.

-	~~{{STRUCTURE_1me5\| PDB=1me5 \| SCENE= }}~~	+	The mechanism of Mycobacterium tuberculosis alkylhydroperoxidase AhpD as defined by mutagenesis, crystallography, and kinetics.,Koshkin A, Nunn CM, Djordjevic S, Ortiz de Montellano PR J Biol Chem. 2003 Aug 8;278(32):29502-8. Epub 2003 May 21. PMID:12761216<ref>PMID:12761216</ref>

-	~~===Crystal Structure~~ of ~~Mycobacterium Tuberculosis Alkylperoxidase AhpD H132Q Mutant===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12761216}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1me5]] is a 3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012761216<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Djordjevic, S.]]		[[Category: Djordjevic, S.]]

OCA: Protected "1me5" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 19:34:35 GMT

Protected "1me5" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:34, 5 December 2012

OCA at 19:34, 5 December 2012

OCA — Wed, 05 Dec 2012 19:34:33 GMT

←Older revision		Revision as of 19:34, 5 December 2012
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-	{{Seed}}
	[[Image:1me5.png\|left\|200px]]		[[Image:1me5.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1me5", 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_1me5\| PDB=1me5 \| SCENE= }}		{{STRUCTURE_1me5\| PDB=1me5 \| SCENE= }}

	===Crystal Structure of Mycobacterium Tuberculosis Alkylperoxidase AhpD H132Q Mutant===		===Crystal Structure of Mycobacterium Tuberculosis Alkylperoxidase AhpD H132Q Mutant===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12761216}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12761216 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12761216}}		{{ABSTRACT_PUBMED_12761216}}

	==About this Structure==		==About this Structure==
-	~~1ME5~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA].	+	[[1me5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME5 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12761216~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012761216</ref><references group="xtra"/>
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
	[[Category: Djordjevic, S.]]		[[Category: Djordjevic, S.]]
Line 29:		Line 17:
	[[Category: Nunn, C M.]]		[[Category: Nunn, C M.]]
	[[Category: Alpha helical]]		[[Category: Alpha helical]]
		+	[[Category: Oxidoreductase]]
	[[Category: Trimer]]		[[Category: Trimer]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:49:53 2009''