5id2 - Revision history

OCA at 13:46, 30 August 2023

OCA — Wed, 30 Aug 2023 13:46:25 GMT

←Older revision		Revision as of 13:46, 30 August 2023
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	<StructureSection load='5id2' size='340' side='right'caption='[[5id2]], [[Resolution\|resolution]] 2.43Å' scene=''>		<StructureSection load='5id2' size='340' side='right'caption='[[5id2]], [[Resolution\|resolution]] 2.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5id2]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ID2 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5ID2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5id2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ID2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ID2 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.43Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~CSO~~:~~S-HYDROXYCYSTEINE~~'>~~CSO~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Rv2238c~~, ~~MtAhpE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])~~<~~/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=5id2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5id2 OCA], [https://pdbe.org/5id2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5id2 RCSB], [https://www.ebi.ac.uk/pdbsum/5id2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5id2 ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15]~~ </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5id2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5id2 OCA], [~~http~~://pdbe.org/5id2 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5id2 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5id2 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5id2 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AHPE_MYCTU AHPE_MYCTU] Thiol-specific peroxidase that catalyzes the reduction of hydrogen peroxide and organic hydroperoxides to water and alcohols, respectively. Plays a role in cell protection against oxidative stress by detoxifying peroxides. May represent an important antioxidant defense against cytotoxic peroxides, especially peroxynitrite, which can be formed by activated macrophages during infection.<ref>PMID:19737009</ref> <ref>PMID:24379404</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu]]~~	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	~~[[Category: Peroxiredoxin~~]]	+	[[Category: Balakrishna AM]]
-	[[Category: Balakrishna~~, A M~~]]	+	[[Category: Gruber G]]
-	[[Category: Gruber, G]]	+	[[Category: Kumar A]]
-	[[Category: Kumar, A]]	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Thioredoxin fold~~]]	+

OCA at 07:13, 3 June 2020

OCA — Wed, 03 Jun 2020 07:13:50 GMT

←Older revision		Revision as of 07:13, 3 June 2020
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	==Asymmetry in the active site of Mycobacterium tuberculosis AhpE upon exposure to Mycothiol==		==Asymmetry in the active site of Mycobacterium tuberculosis AhpE upon exposure to Mycothiol==
-	<StructureSection load='5id2' size='340' side='right' caption='[[5id2]], [[Resolution\|resolution]] 2.43Å' scene=''>	+	<StructureSection load='5id2' size='340' side='right'caption='[[5id2]], [[Resolution\|resolution]] 2.43Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5id2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ID2 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ID2 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5id2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ID2 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ID2 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Rv2238c, MtAhpE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </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=5id2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5id2 OCA], [http://pdbe.org/5id2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5id2 RCSB], [http://www.ebi.ac.uk/pdbsum/5id2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5id2 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5id2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5id2 OCA], [http://pdbe.org/5id2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5id2 RCSB], [http://www.ebi.ac.uk/pdbsum/5id2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5id2 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	==See Also==		==See Also==
-	*[[Thioredoxin ~~Reductase~~\|Thioredoxin ~~Reductase~~]]	+	*[[Thioredoxin reductase 3D structures\|Thioredoxin reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Myctu]]
	[[Category: Peroxiredoxin]]		[[Category: Peroxiredoxin]]
	[[Category: Balakrishna, A M]]		[[Category: Balakrishna, A M]]

OCA at 05:06, 9 September 2016

OCA — Fri, 09 Sep 2016 05:06:41 GMT

←Older revision		Revision as of 05:06, 9 September 2016
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	</div>		</div>
	<div class="pdbe-citations 5id2" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5id2" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thioredoxin Reductase\|Thioredoxin Reductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:59, 4 August 2016

OCA — Thu, 04 Aug 2016 03:59:18 GMT

←Older revision		Revision as of 03:59, 4 August 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5id2 is ~~ON HOLD until Paper~~ Publication	+	==Asymmetry in the active site of Mycobacterium tuberculosis AhpE upon exposure to Mycothiol==
		+	<StructureSection load='5id2' size='340' side='right' caption='[[5id2]], [[Resolution\|resolution]] 2.43Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5id2]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ID2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ID2 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSO:S-HYDROXYCYSTEINE'>CSO</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxiredoxin Peroxiredoxin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.15 1.11.1.15] </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=5id2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5id2 OCA], [http://pdbe.org/5id2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5id2 RCSB], [http://www.ebi.ac.uk/pdbsum/5id2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5id2 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mycobacterium tuberculosis (Mtb) has the ability to persist within the human host for a long time in a dormant stage and re-merges when the immune system is compromised. The pathogenic bacterium employs an elaborate antioxidant defence machinery composed of the mycothiol- and thioredoxin system in addition to a superoxide dismutase, a catalase, and peroxiredoxins (Prxs). Among the family of Peroxiredoxins, Mtb expresses a 1-cysteine peroxiredoxin, known as alkylhydroperoxide reductase E (MtAhpE), and defined as a potential tuberculosis drug target. The reduced MtAhpE (MtAhpE-SH) scavenges peroxides to become converted to MtAhpE-SOH. To provide continuous availability of MtAhpE-SH, MtAhpE-SOH has to become reduced. Here, we used NMR spectroscopy to delineate the reduced (MtAhpE-SH), sulphenic (MtAhpE-SOH) and sulphinic (MtAhpE-SO2H) states of MtAhpE through cysteinyl-labelling, and provide for the first time evidence of a mycothiol-dependent mechanism of MtAhpE reduction. This is confirmed by crystallographic studies, wherein MtAhpE was crystallised in the presence of mycothiol and the structure was solved at 2.43A resolution. Combined with NMR-studies, the crystallographic structures reveal conformational changes of important residues during the catalytic cycle of MtAhpE. In addition, alterations of the overall protein in solution due to redox modulation are observed by small angle X-ray scattering (SAXS) studies. Finally, by employing SAXS and dynamic light scattering, insight is provided into the most probable physiological oligomeric state of MtAhpE necessary for activity, being also discussed in the context of concerted substrate binding inside the dimeric MtAhpE.

-	~~Authors~~:	+	Redox chemistry of Mycobacterium tuberculosis alkylhydroperoxide reductase E (AhpE): Structural and mechanistic insight into a mycoredoxin-1 independent reductive pathway of AhpE via mycothiol.,Kumar A, Balakrishna AM, Nartey W, Manimekalai MS, Gruber G Free Radic Biol Med. 2016 Jul 11. pii: S0891-5849(16)30327-6. doi:, 10.1016/j.freeradbiomed.2016.07.007. PMID:27417938<ref>PMID:27417938</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5id2" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Peroxiredoxin]]
		+	[[Category: Balakrishna, A M]]
		+	[[Category: Gruber, G]]
		+	[[Category: Kumar, A]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Thioredoxin fold]]

OCA at 14:20, 15 May 2016

OCA — Sun, 15 May 2016 14:20:36 GMT

←Older revision		Revision as of 14:20, 15 May 2016
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	The entry 5id2 is ON HOLD until Paper Publication		The entry 5id2 is ON HOLD until Paper Publication

-	Authors: ~~Kumar, A., Balakrishna, A.M., Gruber, G.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kumar, A]]
-	[[Category: Gruber, G]]
-	[[Category: Balakrishna, A.M]]

OCA at 00:24, 11 May 2016

OCA — Wed, 11 May 2016 00:24:11 GMT

←Older revision		Revision as of 00:24, 11 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5id2 is ON HOLD	+	The entry 5id2 is ON HOLD until Paper Publication

-	Authors: Kumar ~~Arvind~~, Balakrishna, A.M., Gruber, G	+	Authors: Kumar, A., Balakrishna, A.M., Gruber, G.

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kumar ~~Arvind, Balakrishna~~, A.M]]	+	[[Category: Kumar, A]]
	[[Category: Gruber, G]]		[[Category: Gruber, G]]
		+	[[Category: Balakrishna, A.M]]

OCA: Protected "5id2" [edit=sysop:move=sysop]

OCA — Wed, 02 Mar 2016 13:45:56 GMT

Protected "5id2" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:45, 2 March 2016

OCA: New page: '''Unreleased structure''' The entry 5id2 is ON HOLD Authors: Kumar Arvind, Balakrishna, A.M., Gruber, G Description: Category: Unreleased Structures [[Category: Kumar Arvind, Bal...

OCA — Wed, 02 Mar 2016 13:45:55 GMT

New page: '''Unreleased structure''' The entry 5id2 is ON HOLD Authors: Kumar Arvind, Balakrishna, A.M., Gruber, G Description: Category: Unreleased Structures [[Category: Kumar Arvind, Bal...

New page

'''Unreleased structure'''

The entry 5id2 is ON HOLD

Authors: Kumar Arvind, Balakrishna, A.M., Gruber, G

Description:
[[Category: Unreleased Structures]]
[[Category: Kumar Arvind, Balakrishna, A.M]]
[[Category: Gruber, G]]