3bq5 - Revision history

OCA at 06:34, 3 April 2024

OCA — Wed, 03 Apr 2024 06:34:54 GMT

←Older revision		Revision as of 06:34, 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=3bq5 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=3bq5 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>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3bq5" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Methionine synthase 3D structures\|Methionine synthase 3D structures]]		*[[Methionine synthase 3D structures\|Methionine synthase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 12:12, 30 August 2023

OCA — Wed, 30 Aug 2023 12:12:42 GMT

←Older revision		Revision as of 12:12, 30 August 2023
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	<StructureSection load='3bq5' size='340' side='right'caption='[[3bq5]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3bq5' size='340' side='right'caption='[[3bq5]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bq5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43589 Atcc 43589~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BQ5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bq5]] 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=3BQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BQ5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=HCS:~~2~~-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1xdj\|1xdj]], [[3bof\|3bof]], [[3bol\|3bol]], [[3bq6\|3bq6]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class="sblockDat">metE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/5-methyltetrahydropteroyltriglutamate--homocysteine_S-methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.14 2.1.1.14] </~~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=3bq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq5 OCA], [https://pdbe.org/3bq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bq5 RCSB], [https://www.ebi.ac.uk/pdbsum/3bq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bq5 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=3bq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq5 OCA], [https://pdbe.org/3bq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bq5 RCSB], [https://www.ebi.ac.uk/pdbsum/3bq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bq5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/METE_THEMA METE_THEMA]] Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity).	+	[https://www.uniprot.org/uniprot/METE_THEMA METE_THEMA] Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</div>		</div>
	<div class="pdbe-citations 3bq5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3bq5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Methionine synthase 3D structures\|Methionine synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]
-	[[Category: Atcc 43589]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ludwig, M L~~]]	+	[[Category: Thermotoga maritima]]
-	[[Category: ~~Pejchal, R~~]]	+	[[Category: Ludwig ML]]
-	[[Category: ~~Smith, J L~~]]	+	[[Category: Pejchal R]]
-	[[Category: ~~Amino-acid biosynthesis]]~~	+	[[Category: Smith JL]]
-	~~[[Category: Homocysteine]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Mete]]~~	+
-	~~[[Category: Methionine biosynthesis]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Tim barrel]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Zinc]]~~	+
-	~~[[Category: Zinc inversion~~]]	+

OCA at 08:21, 19 January 2022

OCA — Wed, 19 Jan 2022 08:21:59 GMT

←Older revision		Revision as of 08:21, 19 January 2022
Line 1:		Line 1:

	==Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine (Monoclinic)==		==Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine (Monoclinic)==
-	<StructureSection load='3bq5' size='340' side='right' caption='[[3bq5]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='3bq5' size='340' side='right'caption='[[3bq5]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bq5]] 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=3BQ5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3BQ5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bq5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43589 Atcc 43589]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BQ5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</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">[[1xdj\|1xdj]], [[3bof\|3bof]], [[3bol\|3bol]], [[3bq6\|3bq6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1xdj\|1xdj]], [[3bof\|3bof]], [[3bol\|3bol]], [[3bq6\|3bq6]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">metE ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">metE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/5-methyltetrahydropteroyltriglutamate--homocysteine_S-methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.14 2.1.1.14] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/5-methyltetrahydropteroyltriglutamate--homocysteine_S-methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.14 2.1.1.14] </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=3bq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq5 OCA], [~~http~~://pdbe.org/3bq5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3bq5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3bq5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3bq5 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=3bq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq5 OCA], [https://pdbe.org/3bq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bq5 RCSB], [https://www.ebi.ac.uk/pdbsum/3bq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bq5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/METE_THEMA METE_THEMA]] Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity).	+	[[https://www.uniprot.org/uniprot/METE_THEMA METE_THEMA]] Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation (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: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]		[[Category: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]
	[[Category: Atcc 43589]]		[[Category: Atcc 43589]]
		+	[[Category: Large Structures]]
	[[Category: Ludwig, M L]]		[[Category: Ludwig, M L]]
	[[Category: Pejchal, R]]		[[Category: Pejchal, R]]

OCA at 08:24, 31 October 2018

OCA — Wed, 31 Oct 2018 08:24:21 GMT

←Older revision		Revision as of 08:24, 31 October 2018
Line 1:		Line 1:
		+
	==Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine (Monoclinic)==		==Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine (Monoclinic)==
	<StructureSection load='3bq5' size='340' side='right' caption='[[3bq5]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3bq5' size='340' side='right' caption='[[3bq5]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">metE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">metE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-methyltetrahydropteroyltriglutamate--homocysteine_S-methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.14 2.1.1.14] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-methyltetrahydropteroyltriglutamate--homocysteine_S-methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.14 2.1.1.14] </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=3bq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq5 OCA], [http://pdbe.org/3bq5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bq5 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq5 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=3bq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq5 OCA], [http://pdbe.org/3bq5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bq5 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bq5 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/bq/3bq5_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bq/3bq5_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 47:		Line 48:
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
	[[Category: Transferase]]		[[Category: Transferase]]
		+	[[Category: Zinc]]
	[[Category: Zinc inversion]]		[[Category: Zinc inversion]]

OCA at 08:37, 8 February 2016

OCA — Mon, 08 Feb 2016 08:37:50 GMT

←Older revision		Revision as of 08:37, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='3bq5' size='340' side='right' caption='[[3bq5]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='3bq5' size='340' side='right' caption='[[3bq5]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3bq5]] 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=3BQ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BQ5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3bq5]] 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=3BQ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BQ5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</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">[[1xdj\|1xdj]], [[3bof\|3bof]], [[3bol\|3bol]], [[3bq6\|3bq6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xdj\|1xdj]], [[3bof\|3bof]], [[3bol\|3bol]], [[3bq6\|3bq6]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">metE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ~~Thermotoga maritima~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">metE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 ATCC 43589])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-methyltetrahydropteroyltriglutamate--homocysteine_S-methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.14 2.1.1.14] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-methyltetrahydropteroyltriglutamate--homocysteine_S-methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.14 2.1.1.14] </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=3bq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bq5 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq5 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=3bq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq5 OCA], [http://pdbe.org/3bq5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bq5 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq5 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<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=3bq5 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 3bq5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]		[[Category: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]
-	[[Category: ~~Thermotoga maritima~~]]	+	[[Category: Atcc 43589]]
	[[Category: Ludwig, M L]]		[[Category: Ludwig, M L]]
	[[Category: Pejchal, R]]		[[Category: Pejchal, R]]

OCA at 22:01, 24 December 2014

OCA — Wed, 24 Dec 2014 22:01:21 GMT

←Older revision		Revision as of 22:01, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3bq5]] 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=3BQ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BQ5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3bq5]] 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=3BQ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BQ5 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xdj\|1xdj]], [[3bof\|3bof]], [[3bol\|3bol]], [[3bq6\|3bq6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xdj\|1xdj]], [[3bof\|3bof]], [[3bol\|3bol]], [[3bq6\|3bq6]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">metE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">metE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-methyltetrahydropteroyltriglutamate--homocysteine_S-methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.14 2.1.1.14] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-methyltetrahydropteroyltriglutamate--homocysteine_S-methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.14 2.1.1.14] </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=3bq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bq5 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq5 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=3bq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bq5 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq5 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/METE_THEMA METE_THEMA]] Catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine resulting in methionine formation (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]		[[Category: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
-	[[Category: Ludwig, M L.]]	+	[[Category: Ludwig, M L]]
-	[[Category: Pejchal, R.]]	+	[[Category: Pejchal, R]]
-	[[Category: Smith, J L.]]	+	[[Category: Smith, J L]]
	[[Category: Amino-acid biosynthesis]]		[[Category: Amino-acid biosynthesis]]
	[[Category: Homocysteine]]		[[Category: Homocysteine]]

OCA at 21:37, 2 October 2014

OCA — Thu, 02 Oct 2014 21:37:11 GMT

←Older revision		Revision as of 21:37, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~3bq5.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine (Monoclinic)==
		+	<StructureSection load='3bq5' size='340' side='right' caption='[[3bq5]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3bq5]] 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=3BQ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BQ5 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=HCS:2-AMINO-4-MERCAPTO-BUTYRIC+ACID'>HCS</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1xdj\|1xdj]], [[3bof\|3bof]], [[3bol\|3bol]], [[3bq6\|3bq6]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">metE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/5-methyltetrahydropteroyltriglutamate--homocysteine_S-methyltransferase 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.14 2.1.1.14] </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=3bq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bq5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bq5 RCSB], [http://www.ebi.ac.uk/pdbsum/3bq5 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/bq/3bq5_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_3bq5\| PDB=3bq5 \| 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>

-	~~===Crystal Structure~~ of T. ~~maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine (Monoclinic)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18296644}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3bq5]] 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=3BQ5 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018296644<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]		[[Category: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]

OCA: Protected "3bq5" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 23:16:45 GMT

Protected "3bq5" [edit=sysop:move=sysop]

←Older revision

Revision as of 23:16, 7 January 2013

OCA at 23:16, 7 January 2013

OCA — Mon, 07 Jan 2013 23:16:43 GMT

←Older revision		Revision as of 23:16, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3bq5.png\|left\|200px]]		[[Image:3bq5.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3bq5", 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_3bq5\| PDB=3bq5 \| SCENE= }}		{{STRUCTURE_3bq5\| PDB=3bq5 \| SCENE= }}

	===Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine (Monoclinic)===		===Crystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine (Monoclinic)===

-
-	<!--
-	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==
-	~~3BQ5~~ 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=3BQ5 OCA].	+	[[3bq5]] 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=3BQ5 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18296644~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018296644</ref><references group="xtra"/>
	[[Category: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]		[[Category: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
Line 37:		Line 25:
	[[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 20:39:51 2009''

OCA at 18:39, 16 February 2009

OCA — Mon, 16 Feb 2009 18:39:53 GMT

←Older revision		Revision as of 18:39, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3BQ5 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=3BQ5 OCA].	+	3BQ5 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=3BQ5 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: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]		[[Category: 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase]]
-	[[Category: Single protein]]
	[[Category: Thermotoga maritima]]		[[Category: Thermotoga maritima]]
	[[Category: Ludwig, M L.]]		[[Category: Ludwig, M L.]]
Line 41:		Line 40:
	[[Category: Zinc inversion]]		[[Category: Zinc inversion]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon ~~Jul 28 00~~:50:~~00 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:39:51 2009''