3bol - Revision history

OCA at 09:30, 21 February 2024

OCA — Wed, 21 Feb 2024 09:30:22 GMT

←Older revision		Revision as of 09:30, 21 February 2024
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	<StructureSection load='3bol' size='340' side='right'caption='[[3bol]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3bol' size='340' side='right'caption='[[3bol]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bol]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43589 Atcc 43589~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3BOL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bol]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BOL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.85Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q7z\|1q7z]], [[3bof\|3bof]], [[3bq5\|3bq5]], [[3bq6\|3bq6]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_synthase Methionine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.13 2.1.1.13] </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=3bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bol OCA], [https://pdbe.org/3bol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bol RCSB], [https://www.ebi.ac.uk/pdbsum/3bol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bol 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=3bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bol OCA], [~~http~~://pdbe.org/3bol PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3bol RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3bol PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3bol ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9WYA5_THEMA Q9WYA5_THEMA]
	== 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=3bol 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=3bol ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

-	Metal active site elasticity linked to activation of homocysteine in methionine synthases.,Koutmos M, Pejchal R, Bomer TM, Matthews RG, Smith JL, Ludwig ML Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3286-91. Epub 2008 Feb 22. PMID:18296644<ref>PMID:18296644</ref>	+	==See Also==
-		+	*[[Methionine synthase 3D structures\|Methionine synthase 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3bol" style="background-color:#fffaf0;"></div>~~	+
-	== ~~References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43589]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Methionine synthase~~]]	+	[[Category: Thermotoga maritima]]
-	[[Category: Koutmos, M]]	+	[[Category: Koutmos M]]
-	[[Category: Ludwig~~, M L~~]]	+	[[Category: Ludwig ML]]
-	[[Category: Smith~~, J L]]~~	+	[[Category: Smith JL]]
-	~~[[Category: Meth]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Tim barrel]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Zinc]]~~	+
-	~~[[Category: Zinc inversion~~]]	+

OCA at 06:19, 5 August 2020

OCA — Wed, 05 Aug 2020 06:19:25 GMT

←Older revision		Revision as of 06:19, 5 August 2020
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	==Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+==		==Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+==
-	<StructureSection load='3bol' size='340' side='right' caption='[[3bol]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='3bol' size='340' side='right'caption='[[3bol]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bol]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BOL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bol]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3BOL FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q7z\|1q7z]], [[3bof\|3bof]], [[3bq5\|3bq5]], [[3bq6\|3bq6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q7z\|1q7z]], [[3bof\|3bof]], [[3bq5\|3bq5]], [[3bq6\|3bq6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_synthase Methionine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.13 2.1.1.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_synthase Methionine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.13 2.1.1.13] </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=3bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bol OCA], [http://pdbe.org/3bol PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bol RCSB], [http://www.ebi.ac.uk/pdbsum/3bol PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bol 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=3bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bol OCA], [http://pdbe.org/3bol PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bol RCSB], [http://www.ebi.ac.uk/pdbsum/3bol PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bol ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 43589]]		[[Category: Atcc 43589]]
		+	[[Category: Large Structures]]
	[[Category: Methionine synthase]]		[[Category: Methionine synthase]]
	[[Category: Koutmos, M]]		[[Category: Koutmos, M]]

OCA at 08:15, 31 October 2018

OCA — Wed, 31 Oct 2018 08:15:51 GMT

←Older revision		Revision as of 08:15, 31 October 2018
Line 1:		Line 1:
		+
	==Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+==		==Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+==
	<StructureSection load='3bol' size='340' side='right' caption='[[3bol]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3bol' size='340' side='right' caption='[[3bol]], [[Resolution\|resolution]] 1.85Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q7z\|1q7z]], [[3bof\|3bof]], [[3bq5\|3bq5]], [[3bq6\|3bq6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q7z\|1q7z]], [[3bof\|3bof]], [[3bq5\|3bq5]], [[3bq6\|3bq6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_synthase Methionine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.13 2.1.1.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_synthase Methionine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.13 2.1.1.13] </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=3bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bol OCA], [http://pdbe.org/3bol PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bol RCSB], [http://www.ebi.ac.uk/pdbsum/3bol 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=3bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bol OCA], [http://pdbe.org/3bol PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bol RCSB], [http://www.ebi.ac.uk/pdbsum/3bol PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bol ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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/bo/3bol_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bo/3bol_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>
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	[[Category: Tim barrel]]		[[Category: Tim barrel]]
	[[Category: Transferase]]		[[Category: Transferase]]
		+	[[Category: Zinc]]
	[[Category: Zinc inversion]]		[[Category: Zinc inversion]]

OCA at 10:10, 8 February 2016

OCA — Mon, 08 Feb 2016 10:10:46 GMT

←Older revision		Revision as of 10:10, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3bol' size='340' side='right' caption='[[3bol]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='3bol' size='340' side='right' caption='[[3bol]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bol]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermotoga_maritima Thermotoga maritima~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BOL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bol]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BOL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q7z\|1q7z]], [[3bof\|3bof]], [[3bq5\|3bq5]], [[3bq6\|3bq6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q7z\|1q7z]], [[3bof\|3bof]], [[3bq5\|3bq5]], [[3bq6\|3bq6]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_synthase Methionine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.13 2.1.1.13] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_synthase Methionine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.13 2.1.1.13] </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=3bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bol OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bol RCSB], [http://www.ebi.ac.uk/pdbsum/3bol 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=3bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bol OCA], [http://pdbe.org/3bol PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bol RCSB], [http://www.ebi.ac.uk/pdbsum/3bol PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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=3bol 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 3bol" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43589]]
	[[Category: Methionine synthase]]		[[Category: Methionine synthase]]
-	[[Category: Thermotoga maritima]]
	[[Category: Koutmos, M]]		[[Category: Koutmos, M]]
	[[Category: Ludwig, M L]]		[[Category: Ludwig, M L]]

OCA at 08:34, 20 January 2015

OCA — Tue, 20 Jan 2015 08:34:38 GMT

←Older revision		Revision as of 08:34, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bol]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BOL FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bol]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BOL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q7z\|1q7z]], [[3bof\|3bof]], [[3bq5\|3bq5]], [[3bq6\|3bq6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q7z\|1q7z]], [[3bof\|3bof]], [[3bq5\|3bq5]], [[3bq6\|3bq6]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_synthase Methionine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.13 2.1.1.13] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_synthase Methionine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.13 2.1.1.13] </span></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=3bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bol OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bol RCSB], [http://www.ebi.ac.uk/pdbsum/3bol 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=3bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bol OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bol RCSB], [http://www.ebi.ac.uk/pdbsum/3bol PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	[[Category: Methionine synthase]]		[[Category: Methionine synthase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
-	[[Category: Koutmos, M.]]	+	[[Category: Koutmos, M]]
-	[[Category: Ludwig, M L.]]	+	[[Category: Ludwig, M L]]
-	[[Category: Smith, J L.]]	+	[[Category: Smith, J L]]
	[[Category: Meth]]		[[Category: Meth]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]

OCA at 21:30, 2 October 2014

OCA — Thu, 02 Oct 2014 21:30:33 GMT

←Older revision		Revision as of 21:30, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~3bol.~~png~~\|~~left~~\|200px]]	+	==Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+==
		+	<StructureSection load='3bol' size='340' side='right' caption='[[3bol]], [[Resolution\|resolution]] 1.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3bol]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BOL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=YT3:YTTRIUM+(III)+ION'>YT3</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1q7z\|1q7z]], [[3bof\|3bof]], [[3bq5\|3bq5]], [[3bq6\|3bq6]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Methionine_synthase Methionine synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.13 2.1.1.13] </span></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=3bol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bol OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bol RCSB], [http://www.ebi.ac.uk/pdbsum/3bol 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/bo/3bol_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 ==
		+	Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

-	~~{{STRUCTURE_3bol\| PDB=3bol \| SCENE= }}~~	+	Metal active site elasticity linked to activation of homocysteine in methionine synthases.,Koutmos M, Pejchal R, Bomer TM, Matthews RG, Smith JL, Ludwig ML Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3286-91. Epub 2008 Feb 22. PMID:18296644<ref>PMID:18296644</ref>

-	~~===Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18296644}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3bol]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermotoga_maritima Thermotoga maritima]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3BOL OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018296644<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Methionine synthase]]		[[Category: Methionine synthase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]

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

OCA — Mon, 07 Jan 2013 18:20:36 GMT

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

←Older revision

Revision as of 18:20, 7 January 2013

OCA at 18:20, 7 January 2013

OCA — Mon, 07 Jan 2013 18:20:34 GMT

←Older revision		Revision as of 18:20, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3bol.png\|left\|200px]]		[[Image:3bol.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3bol", 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_3bol\| PDB=3bol \| SCENE= }}		{{STRUCTURE_3bol\| PDB=3bol \| SCENE= }}

	===Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+===		===Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18296644}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18296644 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18296644}}		{{ABSTRACT_PUBMED_18296644}}

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

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18296644~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018296644</ref><references group="xtra"/>
	[[Category: Methionine synthase]]		[[Category: Methionine synthase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
Line 33:		Line 21:
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
	[[Category: Transferase]]		[[Category: Transferase]]
-	[[Category: Zinc]]
	[[Category: Zinc inversion]]		[[Category: Zinc inversion]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:14:01 2009''

OCA at 19:14, 16 February 2009

OCA — Mon, 16 Feb 2009 19:14:02 GMT

←Older revision		Revision as of 19:14, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3BOL is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOL OCA].	+	3BOL is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BOL OCA].

	==Reference==		==Reference==
-	Metal active site elasticity linked to activation of homocysteine in methionine synthases., Koutmos M, Pejchal R, Bomer TM, Matthews RG, Smith JL, Ludwig ML, Proc Natl Acad Sci U S A. 2008 Mar 4;105(9):3286-91. Epub 2008 Feb 22. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18296644 18296644]~~	+	<ref group="xtra">PMID:18296644</ref><references group="xtra"/>
	[[Category: Methionine synthase]]		[[Category: Methionine synthase]]
-	[[Category: Single protein]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
	[[Category: Koutmos, M.]]		[[Category: Koutmos, M.]]
Line 37:		Line 36:
	[[Category: Zinc inversion]]		[[Category: Zinc inversion]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon ~~Jul 28 02~~:03:~~29 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:14:01 2009''

OCA at 23:03, 27 July 2008

OCA — Sun, 27 Jul 2008 23:03:30 GMT

←Older revision		Revision as of 23:03, 27 July 2008
Line 1:		Line 1:
-	[[Image:3bol.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3bol.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_3bol\| PDB=3bol \| SCENE= }}		{{STRUCTURE_3bol\| PDB=3bol \| SCENE= }}

-	~~'''~~Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+~~'''~~	+	===Cobalamin-dependent methionine synthase (1-566) from Thermotoga maritima complexed with Zn2+===


-	~~==Overview==~~	+	<!--
-	~~Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin~~-~~independent (MetE) and cobalamin~~-~~dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction~~, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, ~~both in~~ the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the ~~protein scaffold accompanies inversion. These structures provide new information~~ on ~~the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases~~. ~~Specifically~~, ~~zinc~~ is ~~mobile in~~ the ~~active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer~~.	+	The line below this paragraph, {{ABSTRACT_PUBMED_18296644}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18296644 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18296644}}

	==About this Structure==		==About this Structure==
Line 32:		Line 36:
	[[Category: Zinc]]		[[Category: Zinc]]
	[[Category: Zinc inversion]]		[[Category: Zinc inversion]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 20~~:57:35 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 02:03:29 2008''