2qbu - Revision history

OCA at 09:15, 21 February 2024

2024-02-21T09:15:09Z

←Older revision		Revision as of 09:15, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2qbu' size='340' side='right'caption='[[2qbu]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2qbu' size='340' side='right'caption='[[2qbu]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qbu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Metth Metth~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QBU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qbu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._Delta_H Methanothermobacter thermautotrophicus str. Delta H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QBU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SAH:S~~-~~ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.1Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~cbil ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=187420 METTH])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></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=2qbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbu OCA], [https://pdbe.org/2qbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qbu RCSB], [https://www.ebi.ac.uk/pdbsum/2qbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qbu 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=2qbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbu OCA], [https://pdbe.org/2qbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qbu RCSB], [https://www.ebi.ac.uk/pdbsum/2qbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qbu ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O27402_METTH O27402_METTH]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 20:
	</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=2qbu 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=2qbu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Ring contraction during cobalamin (vitamin B12) biosynthesis requires a seemingly futile methylation of the C20 position of the tetrapyrrole framework. Along the anaerobic route, this reaction is catalyzed by CbiL, which transfers a methyl group from S-adenosyl-L-methionine to cobalt factor II to generate cobalt factor III. CbiL belongs to the class III methyltransferases and displays similarity to other cobalamin biosynthetic methyltransferases that are responsible for the regiospecific methylation of a number of positions on the tetrapyrrole molecular canvas. In an attempt to understand how CbiL selectively methylates the C20 position, a detailed structure function analysis of the enzyme has been undertaken. In this paper, we demonstrate that the enzyme methylates the C20 position, that its preferred substrate is cobalt factor II, and that the metal ion does not undergo any oxidation change during the course of the reaction. The enzyme was crystallized, and its structure was determined by x-ray crystallography, revealing that the 26-kDa protein has a similar overall topology to other class III enzymes. This helped in the identification of some key amino acid residues (Asp(104), Lys(176), and Tyr(220)). Analysis of mutant variants of these groups has allowed us to suggest potential roles that these side chains may play in substrate binding and catalysis. EPR analysis of binary and ternary complexes indicate that the protein donates a fifth ligand to the cobalt ion via a gated mechanism to prevent transfer of the methyl group to water. The chemical logic underpinning the methylation is discussed.
-
-	Elucidation of substrate specificity in the cobalamin (vitamin B12) biosynthetic methyltransferases. Structure and function of the C20 methyltransferase (CbiL) from Methanothermobacter thermautotrophicus.,Frank S, Deery E, Brindley AA, Leech HK, Lawrence A, Heathcote P, Schubert HL, Brocklehurst K, Rigby SE, Warren MJ, Pickersgill RW J Biol Chem. 2007 Aug 17;282(33):23957-69. Epub 2007 Jun 13. PMID:17567575<ref>PMID:17567575</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2qbu" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Metth~~]]	+	[[Category: Methanothermobacter thermautotrophicus str. Delta H]]
-	[[Category: Frank, S]]	+	[[Category: Frank S]]
-	[[Category: Pickersgill~~, R W~~]]	+	[[Category: Pickersgill RW]]
-	[[Category: Warren~~, M J]]~~	+	[[Category: Warren MJ]]
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:14, 25 June 2021

2021-06-25T08:14:50Z

←Older revision		Revision as of 08:14, 25 June 2021
Line 1:		Line 1:

	==Crystal structure of Methanothermobacter thermautotrophicus CbiL==		==Crystal structure of Methanothermobacter thermautotrophicus CbiL==
-	<StructureSection load='2qbu' size='340' side='right' caption='[[2qbu]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='2qbu' size='340' side='right'caption='[[2qbu]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qbu]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2QBU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qbu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QBU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbil ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbil ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</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=2qbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbu OCA], [~~http~~://pdbe.org/2qbu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2qbu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2qbu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2qbu 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=2qbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbu OCA], [https://pdbe.org/2qbu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qbu RCSB], [https://www.ebi.ac.uk/pdbsum/2qbu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qbu ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Metth]]		[[Category: Metth]]
	[[Category: Frank, S]]		[[Category: Frank, S]]

OCA at 08:31, 29 August 2018

2018-08-29T08:31:35Z

←Older revision		Revision as of 08:31, 29 August 2018
Line 1:		Line 1:
		+
	==Crystal structure of Methanothermobacter thermautotrophicus CbiL==		==Crystal structure of Methanothermobacter thermautotrophicus CbiL==
	<StructureSection load='2qbu' size='340' side='right' caption='[[2qbu]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2qbu' size='340' side='right' caption='[[2qbu]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbil ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbil ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</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=2qbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbu OCA], [http://pdbe.org/2qbu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qbu RCSB], [http://www.ebi.ac.uk/pdbsum/2qbu 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=2qbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbu OCA], [http://pdbe.org/2qbu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qbu RCSB], [http://www.ebi.ac.uk/pdbsum/2qbu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2qbu ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/2qbu_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qb/2qbu_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>

OCA at 04:37, 7 February 2016

2016-02-07T04:37:35Z

←Older revision		Revision as of 04:37, 7 February 2016
Line 15:		Line 15:
	<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=2qbu ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 21:55, 9 September 2015

2015-09-09T21:55:20Z

←Older revision		Revision as of 21:55, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='2qbu' size='340' side='right' caption='[[2qbu]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2qbu' size='340' side='right' caption='[[2qbu]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2qbu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QBU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2qbu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QBU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbil ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~145262 Methanothermobacter thermautotrophicus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbil ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=187420 METTH])</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=2qbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qbu RCSB], [http://www.ebi.ac.uk/pdbsum/2qbu 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=2qbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbu OCA], [http://pdbe.org/2qbu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2qbu RCSB], [http://www.ebi.ac.uk/pdbsum/2qbu PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 2qbu" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Methanothermobacter thermautotrophicus~~]]	+	[[Category: Metth]]
	[[Category: Frank, S]]		[[Category: Frank, S]]
	[[Category: Pickersgill, R W]]		[[Category: Pickersgill, R W]]

OCA at 15:22, 19 January 2015

2015-01-19T15:22:44Z

←Older revision		Revision as of 15:22, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2qbu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QBU FirstGlance]. <br>		<table><tr><td colspan='2'>[[2qbu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QBU FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbil ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbil ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</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=2qbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qbu RCSB], [http://www.ebi.ac.uk/pdbsum/2qbu 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=2qbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qbu RCSB], [http://www.ebi.ac.uk/pdbsum/2qbu 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 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
-	[[Category: Frank, S.]]	+	[[Category: Frank, S]]
-	[[Category: Pickersgill, R W.]]	+	[[Category: Pickersgill, R W]]
-	[[Category: Warren, M J.]]	+	[[Category: Warren, M J]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 18:45, 30 September 2014

2014-09-30T18:45:55Z

←Older revision		Revision as of 18:45, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2qbu.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Methanothermobacter thermautotrophicus CbiL==
		+	<StructureSection load='2qbu' size='340' side='right' caption='[[2qbu]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2qbu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QBU FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cbil ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</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=2qbu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qbu OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qbu RCSB], [http://www.ebi.ac.uk/pdbsum/2qbu 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/qb/2qbu_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 ==
		+	Ring contraction during cobalamin (vitamin B12) biosynthesis requires a seemingly futile methylation of the C20 position of the tetrapyrrole framework. Along the anaerobic route, this reaction is catalyzed by CbiL, which transfers a methyl group from S-adenosyl-L-methionine to cobalt factor II to generate cobalt factor III. CbiL belongs to the class III methyltransferases and displays similarity to other cobalamin biosynthetic methyltransferases that are responsible for the regiospecific methylation of a number of positions on the tetrapyrrole molecular canvas. In an attempt to understand how CbiL selectively methylates the C20 position, a detailed structure function analysis of the enzyme has been undertaken. In this paper, we demonstrate that the enzyme methylates the C20 position, that its preferred substrate is cobalt factor II, and that the metal ion does not undergo any oxidation change during the course of the reaction. The enzyme was crystallized, and its structure was determined by x-ray crystallography, revealing that the 26-kDa protein has a similar overall topology to other class III enzymes. This helped in the identification of some key amino acid residues (Asp(104), Lys(176), and Tyr(220)). Analysis of mutant variants of these groups has allowed us to suggest potential roles that these side chains may play in substrate binding and catalysis. EPR analysis of binary and ternary complexes indicate that the protein donates a fifth ligand to the cobalt ion via a gated mechanism to prevent transfer of the methyl group to water. The chemical logic underpinning the methylation is discussed.

-	~~{{STRUCTURE_2qbu\| PDB=2qbu \| SCENE= }}~~	+	Elucidation of substrate specificity in the cobalamin (vitamin B12) biosynthetic methyltransferases. Structure and function of the C20 methyltransferase (CbiL) from Methanothermobacter thermautotrophicus.,Frank S, Deery E, Brindley AA, Leech HK, Lawrence A, Heathcote P, Schubert HL, Brocklehurst K, Rigby SE, Warren MJ, Pickersgill RW J Biol Chem. 2007 Aug 17;282(33):23957-69. Epub 2007 Jun 13. PMID:17567575<ref>PMID:17567575</ref>

-	~~===Crystal structure~~ of ~~Methanothermobacter thermautotrophicus CbiL===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17567575}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2qbu]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017567575<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Frank, S.]]		[[Category: Frank, S.]]

OCA: Protected "2qbu" [edit=sysop:move=sysop]

2013-01-07T18:42:59Z

Protected "2qbu" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:42, 7 January 2013

OCA at 18:42, 7 January 2013

2013-01-07T18:42:51Z

←Older revision		Revision as of 18:42, 7 January 2013
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-	{{Seed}}
	[[Image:2qbu.png\|left\|200px]]		[[Image:2qbu.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_2qbu\| PDB=2qbu \| SCENE= }}		{{STRUCTURE_2qbu\| PDB=2qbu \| SCENE= }}

	===Crystal structure of Methanothermobacter thermautotrophicus CbiL===		===Crystal structure of Methanothermobacter thermautotrophicus CbiL===

-
-	<!--
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	{{ABSTRACT_PUBMED_17567575}}		{{ABSTRACT_PUBMED_17567575}}

	==About this Structure==		==About this Structure==
-	~~2QBU~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA].	+	[[2qbu]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17567575~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017567575</ref><references group="xtra"/>
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Frank, S.]]		[[Category: Frank, S.]]
Line 29:		Line 17:
	[[Category: Warren, M J.]]		[[Category: Warren, M J.]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 11:22:40 2009''~~	+

OCA at 09:22, 16 February 2009

2009-02-16T09:22:41Z

←Older revision		Revision as of 09:22, 16 February 2009
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	==About this Structure==		==About this Structure==
-	2QBU is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA].	+	2QBU is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QBU OCA].

	==Reference==		==Reference==
-	Elucidation of substrate specificity in the cobalamin (vitamin B12) biosynthetic methyltransferases. Structure and function of the C20 methyltransferase (CbiL) from Methanothermobacter thermautotrophicus., Frank S, Deery E, Brindley AA, Leech HK, Lawrence A, Heathcote P, Schubert HL, Brocklehurst K, Rigby SE, Warren MJ, Pickersgill RW, J Biol Chem. 2007 Aug 17;282(33):23957-69. Epub 2007 Jun 13. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17567575 17567575]~~	+	<ref group="xtra">PMID:17567575</ref><references group="xtra"/>
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
-	[[Category: Single protein]]
	[[Category: Frank, S.]]		[[Category: Frank, S.]]
	[[Category: Pickersgill, R W.]]		[[Category: Pickersgill, R W.]]
Line 31:		Line 30:
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 13~~:23:~~08 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:22:40 2009''