3f0o - Revision history

OCA at 06:37, 3 April 2024

OCA — Wed, 03 Apr 2024 06:37:06 GMT

←Older revision		Revision as of 06:37, 3 April 2024
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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=3f0o 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=3f0o ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Bacteria resistant to methylmercury utilize two enzymes (MerA and MerB) to degrade methylmercury to the less toxic elemental mercury. The crucial step is the cleavage of the carbon-mercury bond of methylmercury by the organomercurial lyase (MerB). In this study, we determined high resolution crystal structures of MerB in both the free (1.76-A resolution) and mercury-bound (1.64-A resolution) states. The crystal structure of free MerB is very similar to the NMR structure, but important differences are observed when comparing the two structures. In the crystal structure, an amino-terminal alpha-helix that is not present in the NMR structure makes contact with the core region adjacent to the catalytic site. This interaction between the amino-terminal helix and the core serves to bury the active site of MerB. The crystal structures also provide detailed insights into the mechanism of carbon-mercury bond cleavage by MerB. The structures demonstrate that two conserved cysteines (Cys-96 and Cys-159) play a role in substrate binding, carbon-mercury bond cleavage, and controlled product (ionic mercury) release. In addition, the structures establish that an aspartic acid (Asp-99) in the active site plays a crucial role in the proton transfer step required for the cleavage of the carbon-mercury bond. These findings are an important step in understanding the mechanism of carbon-mercury bond cleavage by MerB.
-
-	Crystal structures of the organomercurial lyase MerB in its free and mercury-bound forms: insights into the mechanism of methylmercury degradation.,Lafrance-Vanasse J, Lefebvre M, Di Lello P, Sygusch J, Omichinski JG J Biol Chem. 2009 Jan 9;284(2):938-44. Epub 2008 Nov 12. PMID:19004822<ref>PMID:19004822</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3f0o" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 00:27, 28 December 2023

OCA — Thu, 28 Dec 2023 00:27:29 GMT

←Older revision		Revision as of 00:27, 28 December 2023
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	<StructureSection load='3f0o' size='340' side='right'caption='[[3f0o]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='3f0o' size='340' side='right'caption='[[3f0o]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3f0o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F0O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3f0o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F0O FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BR:BROMIDE+ION'>BR</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]] 1.76Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1s6l\|1s6l]]~~, [[~~3f0p~~\|~~3f0p~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>merB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Alkylmercury_lyase Alkylmercury lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.2 4.99.1.2]~~ </~~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=3f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0o OCA], [https://pdbe.org/3f0o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f0o RCSB], [https://www.ebi.ac.uk/pdbsum/3f0o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f0o 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=3f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0o OCA], [https://pdbe.org/3f0o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f0o RCSB], [https://www.ebi.ac.uk/pdbsum/3f0o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f0o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MERB_ECOLX MERB_ECOLX]] Cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. One product is Hg(2+), which is subsequently detoxified by the mercuric reductase (By similarity).	+	[https://www.uniprot.org/uniprot/MERB_ECOLX MERB_ECOLX] Cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. One product is Hg(2+), which is subsequently detoxified by the mercuric reductase (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: Alkylmercury lyase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lafrance-Vanasse, J~~]]	+	[[Category: Di Lello P]]
-	[[Category: ~~Lefebvre, M~~]]	+	[[Category: Lafrance-Vanasse J]]
-	[[Category: ~~Lello, P Di~~]]	+	[[Category: Lefebvre M]]
-	[[Category: Omichinski~~, J G~~]]	+	[[Category: Omichinski JG]]
-	[[Category: Sygusch, J]]	+	[[Category: Sygusch J]]
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Merb]]~~	+
-	~~[[Category: Mercuric resistance]]~~	+
-	~~[[Category: Mercury resistance]]~~	+
-	~~[[Category: Organomercurial lyase]]~~	+
-	~~[[Category: Plasmid~~]]	+

OCA at 09:20, 23 February 2022

OCA — Wed, 23 Feb 2022 09:20:52 GMT

OCA at 22:13, 2 December 2018

OCA — Sun, 02 Dec 2018 22:13:33 GMT

←Older revision		Revision as of 22:13, 2 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system==		==Crystal structure of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system==
	<StructureSection load='3f0o' size='340' side='right' caption='[[3f0o]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='3f0o' size='340' side='right' caption='[[3f0o]], [[Resolution\|resolution]] 1.76Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">merB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">merB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alkylmercury_lyase Alkylmercury lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.2 4.99.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alkylmercury_lyase Alkylmercury lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.2 4.99.1.2] </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=3f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0o OCA], [http://pdbe.org/3f0o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3f0o RCSB], [http://www.ebi.ac.uk/pdbsum/3f0o 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=3f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0o OCA], [http://pdbe.org/3f0o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3f0o RCSB], [http://www.ebi.ac.uk/pdbsum/3f0o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3f0o 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/f0/3f0o_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/f0/3f0o_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>
Line 46:		Line 47:
	[[Category: Mercury resistance]]		[[Category: Mercury resistance]]
	[[Category: Organomercurial lyase]]		[[Category: Organomercurial lyase]]
		+	[[Category: Plasmid]]

OCA at 03:44, 7 February 2016

OCA — Sun, 07 Feb 2016 03:44:31 GMT

←Older revision		Revision as of 03:44, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3f0o' size='340' side='right' caption='[[3f0o]], [[Resolution\|resolution]] 1.76Å' scene=''>		<StructureSection load='3f0o' size='340' side='right' caption='[[3f0o]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3f0o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F0O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3f0o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F0O FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s6l\|1s6l]], [[3f0p\|3f0p]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s6l\|1s6l]], [[3f0p\|3f0p]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">merB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">merB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alkylmercury_lyase Alkylmercury lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.2 4.99.1.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alkylmercury_lyase Alkylmercury lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.2 4.99.1.2] </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=3f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3f0o RCSB], [http://www.ebi.ac.uk/pdbsum/3f0o 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=3f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0o OCA], [http://pdbe.org/3f0o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3f0o RCSB], [http://www.ebi.ac.uk/pdbsum/3f0o PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<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=3f0o ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3f0o" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Alkylmercury lyase]]		[[Category: Alkylmercury lyase]]
-	[[Category: Escherichia coli]]
	[[Category: Lafrance-Vanasse, J]]		[[Category: Lafrance-Vanasse, J]]
	[[Category: Lefebvre, M]]		[[Category: Lefebvre, M]]

OCA at 07:36, 24 December 2014

OCA — Wed, 24 Dec 2014 07:36:50 GMT

←Older revision		Revision as of 07:36, 24 December 2014
Line 9:		Line 9:
	<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=3f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3f0o RCSB], [http://www.ebi.ac.uk/pdbsum/3f0o 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=3f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3f0o RCSB], [http://www.ebi.ac.uk/pdbsum/3f0o PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MERB_ECOLX MERB_ECOLX]] Cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. One product is Hg(2+), which is subsequently detoxified by the mercuric reductase (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:55, 26 November 2014

OCA — Wed, 26 Nov 2014 08:55:57 GMT

←Older revision		Revision as of 08:55, 26 November 2014
Line 1:		Line 1:
-	[[~~Image:~~3f0o.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system==
		+	<StructureSection load='3f0o' size='340' side='right' caption='[[3f0o]], [[Resolution\|resolution]] 1.76Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3f0o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3F0O FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s6l\|1s6l]], [[3f0p\|3f0p]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">merB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Alkylmercury_lyase Alkylmercury lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.2 4.99.1.2] </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=3f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3f0o RCSB], [http://www.ebi.ac.uk/pdbsum/3f0o 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/f0/3f0o_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 ==
		+	Bacteria resistant to methylmercury utilize two enzymes (MerA and MerB) to degrade methylmercury to the less toxic elemental mercury. The crucial step is the cleavage of the carbon-mercury bond of methylmercury by the organomercurial lyase (MerB). In this study, we determined high resolution crystal structures of MerB in both the free (1.76-A resolution) and mercury-bound (1.64-A resolution) states. The crystal structure of free MerB is very similar to the NMR structure, but important differences are observed when comparing the two structures. In the crystal structure, an amino-terminal alpha-helix that is not present in the NMR structure makes contact with the core region adjacent to the catalytic site. This interaction between the amino-terminal helix and the core serves to bury the active site of MerB. The crystal structures also provide detailed insights into the mechanism of carbon-mercury bond cleavage by MerB. The structures demonstrate that two conserved cysteines (Cys-96 and Cys-159) play a role in substrate binding, carbon-mercury bond cleavage, and controlled product (ionic mercury) release. In addition, the structures establish that an aspartic acid (Asp-99) in the active site plays a crucial role in the proton transfer step required for the cleavage of the carbon-mercury bond. These findings are an important step in understanding the mechanism of carbon-mercury bond cleavage by MerB.

-	~~{{STRUCTURE_3f0o\| PDB=3f0o \| SCENE= }}~~	+	Crystal structures of the organomercurial lyase MerB in its free and mercury-bound forms: insights into the mechanism of methylmercury degradation.,Lafrance-Vanasse J, Lefebvre M, Di Lello P, Sygusch J, Omichinski JG J Biol Chem. 2009 Jan 9;284(2):938-44. Epub 2008 Nov 12. PMID:19004822<ref>PMID:19004822</ref>

-	~~===Crystal structure~~ of ~~MerB,~~ the ~~Organomercurial Lyase involved in a bacterial mercury resistance system===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19004822}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3f0o]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019004822<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Alkylmercury lyase]]		[[Category: Alkylmercury lyase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Lafrance-Vanasse, J.]]	+	[[Category: Lafrance-Vanasse, J]]
-	[[Category: Lefebvre, M.]]	+	[[Category: Lefebvre, M]]
-	[[Category: Lello, P Di.]]	+	[[Category: Lello, P Di]]
-	[[Category: Omichinski, J G.]]	+	[[Category: Omichinski, J G]]
-	[[Category: Sygusch, J~~.]]~~	+	[[Category: Sygusch, J]]
-	~~[[Category: Alkylmercury lyase~~]]	+
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Merb]]		[[Category: Merb]]

OCA: Protected "3f0o" [edit=sysop:move=sysop]

OCA — Wed, 13 Feb 2013 11:22:11 GMT

Protected "3f0o" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:22, 13 February 2013

OCA at 11:22, 13 February 2013

OCA — Wed, 13 Feb 2013 11:22:08 GMT

←Older revision		Revision as of 11:22, 13 February 2013
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-	{{Seed}}
	[[Image:3f0o.png\|left\|200px]]		[[Image:3f0o.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_3f0o\| PDB=3f0o \| SCENE= }}		{{STRUCTURE_3f0o\| PDB=3f0o \| SCENE= }}

	===Crystal structure of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system===		===Crystal structure of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19004822}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_19004822}}		{{ABSTRACT_PUBMED_19004822}}

	==About this Structure==		==About this Structure==
-	~~3F0O~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA].	+	[[3f0o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19004822~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019004822</ref><references group="xtra"/>
	[[Category: Alkylmercury lyase]]		[[Category: Alkylmercury lyase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 32:		Line 20:
	[[Category: Sygusch, J.]]		[[Category: Sygusch, J.]]
	[[Category: Alkylmercury lyase]]		[[Category: Alkylmercury lyase]]
		+	[[Category: Lyase]]
	[[Category: Merb]]		[[Category: Merb]]
	[[Category: Mercuric resistance]]		[[Category: Mercuric resistance]]
	[[Category: Mercury resistance]]		[[Category: Mercury resistance]]
	[[Category: Organomercurial lyase]]		[[Category: Organomercurial lyase]]
-	[[Category: Plasmid]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 10:57:51 2009''

OCA at 08:57, 16 February 2009

OCA — Mon, 16 Feb 2009 08:57:52 GMT

←Older revision		Revision as of 08:57, 16 February 2009
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	==About this Structure==		==About this Structure==
-	3F0O is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA].	+	3F0O is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA].

	==Reference==		==Reference==
-	Crystal Structures of the Organomercurial Lyase MerB in Its Free and Mercury-bound Forms: INSIGHTS INTO THE MECHANISM OF METHYLMERCURY DEGRADATION., Lafrance-Vanasse J, Lefebvre M, Di Lello P, Sygusch J, Omichinski JG, J Biol Chem. 2009 Jan 9;284(2):938-44. Epub 2008 Nov 12. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/19004822 19004822]~~	+	<ref group="xtra">PMID:19004822</ref><references group="xtra"/>
	[[Category: Alkylmercury lyase]]		[[Category: Alkylmercury lyase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: ~~Single protein~~]]	+	[[Category: Lafrance-Vanasse, J.]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]	+	[[Category: Lefebvre, M.]]
		+	[[Category: Lello, P Di.]]
		+	[[Category: Omichinski, J G.]]
		+	[[Category: Sygusch, J.]]
	[[Category: Alkylmercury lyase]]		[[Category: Alkylmercury lyase]]
	[[Category: Merb]]		[[Category: Merb]]
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	[[Category: Plasmid]]		[[Category: Plasmid]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jan 21 20~~:34:29 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 10:57:51 2009''

←Older revision		Revision as of 09:20, 23 February 2022
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	==Crystal structure of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system==		==Crystal structure of MerB, the Organomercurial Lyase involved in a bacterial mercury resistance system==
-	<StructureSection load='3f0o' size='340' side='right' caption='[[3f0o]], [[Resolution\|resolution]] 1.76Å' scene=''>	+	<StructureSection load='3f0o' size='340' side='right'caption='[[3f0o]], [[Resolution\|resolution]] 1.76Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3f0o]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3F0O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3f0o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3F0O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3F0O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1s6l\|1s6l]], [[3f0p\|3f0p]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1s6l\|1s6l]], [[3f0p\|3f0p]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">merB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">merB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Alkylmercury_lyase Alkylmercury lyase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.2 4.99.1.2] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Alkylmercury_lyase Alkylmercury lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.99.1.2 4.99.1.2] </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=3f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0o OCA], [~~http~~://pdbe.org/3f0o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3f0o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3f0o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3f0o 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=3f0o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3f0o OCA], [https://pdbe.org/3f0o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3f0o RCSB], [https://www.ebi.ac.uk/pdbsum/3f0o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3f0o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MERB_ECOLX MERB_ECOLX]] Cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. One product is Hg(2+), which is subsequently detoxified by the mercuric reductase (By similarity).	+	[[https://www.uniprot.org/uniprot/MERB_ECOLX MERB_ECOLX]] Cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. One product is Hg(2+), which is subsequently detoxified by the mercuric reductase (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Alkylmercury lyase]]		[[Category: Alkylmercury lyase]]
		+	[[Category: Large Structures]]
	[[Category: Lafrance-Vanasse, J]]		[[Category: Lafrance-Vanasse, J]]
	[[Category: Lefebvre, M]]		[[Category: Lefebvre, M]]