4x0x - Revision history

OCA at 10:45, 10 January 2024

OCA — Wed, 10 Jan 2024 10:45:47 GMT

←Older revision		Revision as of 10:45, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4x0x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_CDC1551 Mycobacterium tuberculosis CDC1551]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X0X FirstGlance]. <br>		<table><tr><td colspan='2'>[[4x0x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_CDC1551 Mycobacterium tuberculosis CDC1551]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X0X FirstGlance]. <br>
-	</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=4x0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0x OCA], [https://pdbe.org/4x0x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x0x RCSB], [https://www.ebi.ac.uk/pdbsum/4x0x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0x ProSAT]</span></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]] 1.9Å</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=4x0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0x OCA], [https://pdbe.org/4x0x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x0x RCSB], [https://www.ebi.ac.uk/pdbsum/4x0x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 21:06, 12 April 2023

OCA — Wed, 12 Apr 2023 21:06:17 GMT

←Older revision		Revision as of 21:06, 12 April 2023
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	<StructureSection load='4x0x' size='340' side='right'caption='[[4x0x]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='4x0x' size='340' side='right'caption='[[4x0x]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x0x]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Mycto Mycto~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4X0X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x0x]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_CDC1551 Mycobacterium tuberculosis CDC1551]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X0X FirstGlance]. <br>
-	</td></tr>~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MT2298 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83331 MYCTO])</td></tr>~~	+	</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=4x0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0x OCA], [https://pdbe.org/4x0x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x0x RCSB], [https://www.ebi.ac.uk/pdbsum/4x0x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0x 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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4x0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0x OCA], [~~http~~://pdbe.org/4x0x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4x0x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4x0x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0x ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/AHPE_MYCTO AHPE_MYCTO] 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.[UniProtKB:P9WIE3]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Thioredoxin ~~Reductase~~\|Thioredoxin ~~Reductase~~]]	+	*[[Thioredoxin reductase 3D structures\|Thioredoxin reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Mycto]]~~	+	[[Category: Mycobacterium tuberculosis CDC1551]]
-	~~[[Category: Peroxiredoxin~~]]	+	[[Category: Messens J]]
-	[[Category: Messens, J]]	+	[[Category: Pallo A]]
-	[[Category: Pallo, A]]	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Protein structure~~]]	+

OCA at 07:54, 23 May 2019

OCA — Thu, 23 May 2019 07:54:35 GMT

←Older revision		Revision as of 07:54, 23 May 2019
Line 1:		Line 1:

	==The structure of AhpE from Mycobacterium tuberculosis revisited==		==The structure of AhpE from Mycobacterium tuberculosis revisited==
-	<StructureSection load='4x0x' size='340' side='right' caption='[[4x0x]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='4x0x' size='340' side='right'caption='[[4x0x]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4x0x]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4x0x]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycto Mycto]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0X FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MT2298 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83331 MYCTO])</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=4x0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0x OCA], [http://pdbe.org/4x0x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x0x RCSB], [http://www.ebi.ac.uk/pdbsum/4x0x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0x 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=4x0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0x OCA], [http://pdbe.org/4x0x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x0x RCSB], [http://www.ebi.ac.uk/pdbsum/4x0x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0x ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mycto]]
	[[Category: Peroxiredoxin]]		[[Category: Peroxiredoxin]]
	[[Category: Messens, J]]		[[Category: Messens, J]]

OCA at 17:04, 9 September 2016

OCA — Fri, 09 Sep 2016 17:04:27 GMT

←Older revision		Revision as of 17:04, 9 September 2016
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 4x0x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4x0x" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thioredoxin Reductase\|Thioredoxin Reductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:55, 10 August 2016

OCA — Wed, 10 Aug 2016 07:55:10 GMT

←Older revision		Revision as of 07:55, 10 August 2016
Line 9:		Line 9:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~All living systems require protection against the damaging effects of reactive oxygen species. The genome of Mycobacterium tuberculosis~~, ~~the cause~~ of ~~TB, encodes a number~~ of ~~peroxidases that are thought~~ to ~~be active against organic and inorganic peroxides, and are likely to play a key role in~~ the ~~ability of this organism to survive within the phagosomes of macrophages. The open reading frame Rv2238c in M.tuberculosis encodes a 153~~-~~residue protein AhpE~~, which ~~is a peroxidase~~ of the 1-~~Cys peroxiredoxin (Prx) family~~. ~~The crystal structure~~ of ~~AhpE, determined at 1.87 A resolution (R(cryst)=0.179, R(free)=0.210), reveals~~ a ~~compact~~ single-~~domain protein with a thioredoxin fold~~. ~~AhpE forms both dimers and octamers;~~ a ~~tightly~~-~~associated dimer~~ and a ~~ring~~-~~like octamer, generated by crystallographic 4-fold symmetry~~. ~~In this native structure,~~ the ~~active site Cys45 is in its oxidized, sulfenic acid~~ (~~S-O-H~~) ~~state. A second crystal form of AhpE~~, ~~obtained after soaking in sodium bromide~~ and ~~refined at 1~~.~~90 A resolution (R(cryst)=0.242~~, ~~R(free)=0.286)~~, ~~reveals~~ the ~~reduced structure~~. In ~~this structure~~, ~~a conformational change in an external loop~~, ~~in two~~ of the ~~four molecules~~ in ~~the asymmetric unit, allows Arg116 to stabilise the Cys45 thiolate ion, and concomitantly closes a surface channel. This channel~~ is ~~identified as the likely binding site for a physiological reductant, and the conformational change is inferred to be important for the reaction cycle of AhpE~~.	+	In many established methods, identification of hydrogen bonds (H-bonds) is primarily based on pairwise comparison of distances between atoms. These methods often give rise to systematic errors when sulfur is involved. A more accurate method is the non-covalent interaction index, which determines the strength of the H-bonds based on the associated electron density and its gradient. We applied the NCI index on the active site of a single-cysteine peroxiredoxin. We found a different sulfur hydrogen-bonding network to that typically found by established methods, and we propose a more accurate equation for determining sulfur H-bonds based on geometrical criteria. This new algorithm will be implemented in the next release of the widely-used CHARMM program (version 41b), and will be particularly useful for analyzing water molecule-mediated H-bonds involving different atom types. Furthermore, based on the identification of the weakest sulfur-water H-bond, the location of hydrogen peroxide for the nucleophilic attack by the cysteine sulfur can be predicted. In general, current methods to determine H-bonds will need to be reevaluated, thereby leading to better understanding of the catalytic mechanisms in which sulfur chemistry is involved.

-	~~Crystal Structure~~ of AhpE ~~from Mycobacterium tuberculosis, a 1-Cys peroxiredoxin~~.,~~Li S~~, ~~Peterson NA, Kim MY, Kim CY, Hung LW, Yu~~ M, ~~Lekin T~~, ~~Segelke BW~~, ~~Lott JS~~, ~~Baker EN~~ J ~~Mol Biol~~. ~~2005 Mar 4~~;~~346(4)~~:~~1035-46~~. ~~Epub 2005 Jan 25~~. PMID:~~15701515~~<ref>PMID:~~15701515~~</ref>	+	Revisiting sulfur H-bonds in proteins: The example of peroxiredoxin AhpE.,van Bergen LA, Alonso M, Pallo A, Nilsson L, De Proft F, Messens J Sci Rep. 2016 Jul 29;6:30369. doi: 10.1038/srep30369. PMID:27468924<ref>PMID:27468924</ref>

	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>

OCA at 15:32, 27 July 2016

OCA — Wed, 27 Jul 2016 15:32:15 GMT

←Older revision		Revision as of 15:32, 27 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 4x0x is ~~ON HOLD~~	+	==The structure of AhpE from Mycobacterium tuberculosis revisited==
		+	<StructureSection load='4x0x' size='340' side='right' caption='[[4x0x]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4x0x]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X0X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X0X FirstGlance]. <br>
		+	</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=4x0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x0x OCA], [http://pdbe.org/4x0x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x0x RCSB], [http://www.ebi.ac.uk/pdbsum/4x0x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x0x ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	All living systems require protection against the damaging effects of reactive oxygen species. The genome of Mycobacterium tuberculosis, the cause of TB, encodes a number of peroxidases that are thought to be active against organic and inorganic peroxides, and are likely to play a key role in the ability of this organism to survive within the phagosomes of macrophages. The open reading frame Rv2238c in M.tuberculosis encodes a 153-residue protein AhpE, which is a peroxidase of the 1-Cys peroxiredoxin (Prx) family. The crystal structure of AhpE, determined at 1.87 A resolution (R(cryst)=0.179, R(free)=0.210), reveals a compact single-domain protein with a thioredoxin fold. AhpE forms both dimers and octamers; a tightly-associated dimer and a ring-like octamer, generated by crystallographic 4-fold symmetry. In this native structure, the active site Cys45 is in its oxidized, sulfenic acid (S-O-H) state. A second crystal form of AhpE, obtained after soaking in sodium bromide and refined at 1.90 A resolution (R(cryst)=0.242, R(free)=0.286), reveals the reduced structure. In this structure, a conformational change in an external loop, in two of the four molecules in the asymmetric unit, allows Arg116 to stabilise the Cys45 thiolate ion, and concomitantly closes a surface channel. This channel is identified as the likely binding site for a physiological reductant, and the conformational change is inferred to be important for the reaction cycle of AhpE.

-	~~Authors: Pallo~~, A., ~~Messens~~, J.	+	Crystal Structure of AhpE from Mycobacterium tuberculosis, a 1-Cys peroxiredoxin.,Li S, Peterson NA, Kim MY, Kim CY, Hung LW, Yu M, Lekin T, Segelke BW, Lott JS, Baker EN J Mol Biol. 2005 Mar 4;346(4):1035-46. Epub 2005 Jan 25. PMID:15701515<ref>PMID:15701515</ref>

-	~~Description: The structure~~ of ~~AhpE from Mycobacterium tuberculosis revisited~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Pallo, A~~]]	+	<div class="pdbe-citations 4x0x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Peroxiredoxin]]
	[[Category: Messens, J]]		[[Category: Messens, J]]
		+	[[Category: Pallo, A]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Protein structure]]

OCA at 20:18, 24 December 2014

OCA — Wed, 24 Dec 2014 20:18:45 GMT

←Older revision		Revision as of 20:18, 24 December 2014
Line 6:		Line 6:

	Description: The structure of AhpE from Mycobacterium tuberculosis revisited		Description: The structure of AhpE from Mycobacterium tuberculosis revisited
		+	[[Category: Unreleased Structures]]
		+	[[Category: Pallo, A]]
		+	[[Category: Messens, J]]

OCA: Protected "4x0x" [edit=sysop:move=sysop]

OCA — Wed, 03 Dec 2014 08:44:37 GMT

Protected "4x0x" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:44, 3 December 2014

OCA: New page: '''Unreleased structure''' The entry 4x0x is ON HOLD Authors: Pallo, A., Messens, J. Description: The structure of AhpE from Mycobacterium tuberculosis revisited

OCA — Wed, 03 Dec 2014 08:44:36 GMT

New page: '''Unreleased structure''' The entry 4x0x is ON HOLD Authors: Pallo, A., Messens, J. Description: The structure of AhpE from Mycobacterium tuberculosis revisited

New page

'''Unreleased structure'''

The entry 4x0x is ON HOLD

Authors: Pallo, A., Messens, J.

Description: The structure of AhpE from Mycobacterium tuberculosis revisited