3gaj - Revision history

OCA at 09:53, 21 February 2024

OCA — Wed, 21 Feb 2024 09:53:32 GMT

←Older revision		Revision as of 09:53, 21 February 2024
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	<StructureSection load='3gaj' size='340' side='right'caption='[[3gaj]], [[Resolution\|resolution]] 1.38Å' scene=''>		<StructureSection load='3gaj' size='340' side='right'caption='[[3gaj]], [[Resolution\|resolution]] 1.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gaj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_23272 Atcc 23272~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GAJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gaj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Limosilactobacillus_reuteri Limosilactobacillus reuteri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GAJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.38Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA, pduo ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1598 ATCC 23272])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cob(I)yrinic_acid_a,c-diamide_adenosyltransferase Cob(I)yrinic acid a,c-diamide adenosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.17 2.5.1.17] </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=3gaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gaj OCA], [https://pdbe.org/3gaj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gaj RCSB], [https://www.ebi.ac.uk/pdbsum/3gaj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gaj 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=3gaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gaj OCA], [https://pdbe.org/3gaj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gaj RCSB], [https://www.ebi.ac.uk/pdbsum/3gaj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gaj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q50EJ2_LIMRT Q50EJ2_LIMRT]
	== 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=3gaj 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=3gaj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	ATP:Corrinoid adenosyltransferases (ACAs) catalyze the transfer of the adenosyl moiety from ATP to cob(I)alamin via a four-coordinate cob(II)alamin intermediate. At present, it is unknown how ACAs promote the formation of the four-coordinate corrinoid species needed for activity. The published high-resolution crystal structure of the ACA from Lactobacillus reuteri (LrPduO) in complex with ATP and cob(II)alamin shows that the environment around the alpha face of the corrin ring consists of bulky hydrophobic residues. To understand how these residues promote the generation of the four-coordinate cob(II)alamin, variants of the human-type ACA enzyme from L. reuteri (LrPduO) were kinetically and structurally characterized. These studies revealed that residue Phe112 is critical in the displacement of 5,6-dimethylbenzimidazole (DMB) from its coordination bond with the Co ion of the ring, resulting in the formation of the four-coordinate species. An F112A substitution resulted in a 80% drop in the catalytic efficiency of the enzyme. The explanation for this loss of activity was obtained from the crystal structure of the mutant protein, which showed cob(II)alamin bound in the active site with DMB coordinated to the cobalt ion. The crystal structure of an LrPduO(F112H) variant showed a DMB-off/His-on interaction between the corrinoid and the enzyme, whose catalytic efficiency was 4 orders of magnitude lower than that of the wild-type protein. The analysis of the kinetic parameters of LrPduO(F112H) suggests that the F112H substitution negatively impacts product release. Substitutions of other hydrophobic residues in the Cbl binding pocket did not result in significant defects in catalytic efficiency in vitro; however, none of the variant enzymes analyzed in this work supported AdoCbl biosynthesis in vivo.
-
-	Residue Phe112 of the human-type corrinoid adenosyltransferase (PduO) enzyme of Lactobacillus reuteri is critical to the formation of the four-coordinate Co(II) corrinoid substrate and to the activity of the enzyme.,Mera PE, St Maurice M, Rayment I, Escalante-Semerena JC Biochemistry. 2009 Apr 14;48(14):3138-45. PMID:19236001<ref>PMID:19236001</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3gaj" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 23272]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Escalante-Semerena, J C~~]]	+	[[Category: Limosilactobacillus reuteri]]
-	[[Category: ~~Maurice, M St~~]]	+	[[Category: Escalante-Semerena JC]]
-	[[Category: Mera~~, P E~~]]	+	[[Category: Mera PE]]
-	[[Category: Rayment, I]]	+	[[Category: Rayment I]]
-	[[Category: ~~Transferase~~]]	+	[[Category: St Maurice M]]

OCA at 08:00, 9 March 2022

OCA — Wed, 09 Mar 2022 08:00:14 GMT

←Older revision		Revision as of 08:00, 9 March 2022
Line 1:		Line 1:

	==Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP==		==Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP==
-	<StructureSection load='3gaj' size='340' side='right' caption='[[3gaj]], [[Resolution\|resolution]] 1.38Å' scene=''>	+	<StructureSection load='3gaj' size='340' side='right'caption='[[3gaj]], [[Resolution\|resolution]] 1.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gaj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_23272 Atcc 23272]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3GAJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gaj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_23272 Atcc 23272]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GAJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA, pduo ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1598 ATCC 23272])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA, pduo ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1598 ATCC 23272])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Cob(I)yrinic_acid_a,c-diamide_adenosyltransferase Cob(I)yrinic acid a,c-diamide adenosyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.17 2.5.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cob(I)yrinic_acid_a,c-diamide_adenosyltransferase Cob(I)yrinic acid a,c-diamide adenosyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.17 2.5.1.17] </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=3gaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gaj OCA], [~~http~~://pdbe.org/3gaj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3gaj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3gaj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3gaj 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=3gaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gaj OCA], [https://pdbe.org/3gaj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gaj RCSB], [https://www.ebi.ac.uk/pdbsum/3gaj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gaj ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ga/3gaj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ga/3gaj_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 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 23272]]		[[Category: Atcc 23272]]
		+	[[Category: Large Structures]]
	[[Category: Escalante-Semerena, J C]]		[[Category: Escalante-Semerena, J C]]
	[[Category: Maurice, M St]]		[[Category: Maurice, M St]]

OCA at 15:04, 11 August 2016

OCA — Thu, 11 Aug 2016 15:04:04 GMT

←Older revision		Revision as of 15:04, 11 August 2016
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		+
	==Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP==		==Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP==
	<StructureSection load='3gaj' size='340' side='right' caption='[[3gaj]], [[Resolution\|resolution]] 1.38Å' scene=''>		<StructureSection load='3gaj' size='340' side='right' caption='[[3gaj]], [[Resolution\|resolution]] 1.38Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3gaj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Lactobacillus_reuteri Lactobacillus reuteri~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GAJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3gaj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_23272 Atcc 23272]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GAJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA, pduo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1598 ~~Lactobacillus reuteri~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA, pduo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1598 ATCC 23272])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cob(I)yrinic_acid_a,c-diamide_adenosyltransferase Cob(I)yrinic acid a,c-diamide adenosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.17 2.5.1.17] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cob(I)yrinic_acid_a,c-diamide_adenosyltransferase Cob(I)yrinic acid a,c-diamide adenosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.17 2.5.1.17] </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=3gaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gaj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gaj RCSB], [http://www.ebi.ac.uk/pdbsum/3gaj 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=3gaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gaj OCA], [http://pdbe.org/3gaj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3gaj RCSB], [http://www.ebi.ac.uk/pdbsum/3gaj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3gaj ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<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=3gaj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	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 3gaj" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lactobacillus reuteri~~]]	+	[[Category: Atcc 23272]]
	[[Category: Escalante-Semerena, J C]]		[[Category: Escalante-Semerena, J C]]
	[[Category: Maurice, M St]]		[[Category: Maurice, M St]]

OCA at 08:54, 20 January 2015

OCA — Tue, 20 Jan 2015 08:54:16 GMT

←Older revision		Revision as of 08:54, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3gaj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_reuteri Lactobacillus reuteri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GAJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[3gaj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_reuteri Lactobacillus reuteri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GAJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA, pduo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1598 Lactobacillus reuteri])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA, pduo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1598 Lactobacillus reuteri])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cob(I)yrinic_acid_a,c-diamide_adenosyltransferase Cob(I)yrinic acid a,c-diamide adenosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.17 2.5.1.17] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cob(I)yrinic_acid_a,c-diamide_adenosyltransferase Cob(I)yrinic acid a,c-diamide adenosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.17 2.5.1.17] </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=3gaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gaj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gaj RCSB], [http://www.ebi.ac.uk/pdbsum/3gaj 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=3gaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gaj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gaj RCSB], [http://www.ebi.ac.uk/pdbsum/3gaj 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 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Lactobacillus reuteri]]		[[Category: Lactobacillus reuteri]]
-	[[Category: Escalante-Semerena, J C.]]	+	[[Category: Escalante-Semerena, J C]]
-	[[Category: Maurice, M St.]]	+	[[Category: Maurice, M St]]
-	[[Category: Mera, P E.]]	+	[[Category: Mera, P E]]
-	[[Category: Rayment, I.]]	+	[[Category: Rayment, I]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 12:45, 29 September 2014

OCA — Mon, 29 Sep 2014 12:45:39 GMT

←Older revision		Revision as of 12:45, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3gaj.~~png~~\|~~left~~\|200px]]	+	==Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP==
		+	<StructureSection load='3gaj' size='340' side='right' caption='[[3gaj]], [[Resolution\|resolution]] 1.38Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3gaj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_reuteri Lactobacillus reuteri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3GAJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA, pduo ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1598 Lactobacillus reuteri])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cob(I)yrinic_acid_a,c-diamide_adenosyltransferase Cob(I)yrinic acid a,c-diamide adenosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.17 2.5.1.17] </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=3gaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gaj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3gaj RCSB], [http://www.ebi.ac.uk/pdbsum/3gaj 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/ga/3gaj_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 ==
		+	ATP:Corrinoid adenosyltransferases (ACAs) catalyze the transfer of the adenosyl moiety from ATP to cob(I)alamin via a four-coordinate cob(II)alamin intermediate. At present, it is unknown how ACAs promote the formation of the four-coordinate corrinoid species needed for activity. The published high-resolution crystal structure of the ACA from Lactobacillus reuteri (LrPduO) in complex with ATP and cob(II)alamin shows that the environment around the alpha face of the corrin ring consists of bulky hydrophobic residues. To understand how these residues promote the generation of the four-coordinate cob(II)alamin, variants of the human-type ACA enzyme from L. reuteri (LrPduO) were kinetically and structurally characterized. These studies revealed that residue Phe112 is critical in the displacement of 5,6-dimethylbenzimidazole (DMB) from its coordination bond with the Co ion of the ring, resulting in the formation of the four-coordinate species. An F112A substitution resulted in a 80% drop in the catalytic efficiency of the enzyme. The explanation for this loss of activity was obtained from the crystal structure of the mutant protein, which showed cob(II)alamin bound in the active site with DMB coordinated to the cobalt ion. The crystal structure of an LrPduO(F112H) variant showed a DMB-off/His-on interaction between the corrinoid and the enzyme, whose catalytic efficiency was 4 orders of magnitude lower than that of the wild-type protein. The analysis of the kinetic parameters of LrPduO(F112H) suggests that the F112H substitution negatively impacts product release. Substitutions of other hydrophobic residues in the Cbl binding pocket did not result in significant defects in catalytic efficiency in vitro; however, none of the variant enzymes analyzed in this work supported AdoCbl biosynthesis in vivo.

-	~~{{STRUCTURE_3gaj\| PDB=3gaj \| SCENE= }}~~	+	Residue Phe112 of the human-type corrinoid adenosyltransferase (PduO) enzyme of Lactobacillus reuteri is critical to the formation of the four-coordinate Co(II) corrinoid substrate and to the activity of the enzyme.,Mera PE, St Maurice M, Rayment I, Escalante-Semerena JC Biochemistry. 2009 Apr 14;48(14):3138-45. PMID:19236001<ref>PMID:19236001</ref>

-	~~===Structure of~~ a ~~C-terminal deletion variant~~ of ~~a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19236001}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3gaj]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Lactobacillus_reuteri Lactobacillus reuteri]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019236001<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Lactobacillus reuteri]]		[[Category: Lactobacillus reuteri]]
	[[Category: Escalante-Semerena, J C.]]		[[Category: Escalante-Semerena, J C.]]

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

OCA — Wed, 24 Oct 2012 06:27:01 GMT

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

←Older revision

Revision as of 06:27, 24 October 2012

OCA at 06:27, 24 October 2012

OCA — Wed, 24 Oct 2012 06:27:00 GMT

←Older revision		Revision as of 06:27, 24 October 2012
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3gaj.png\|left\|200px]]
-	[[Image:3gaj.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3gaj", 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_3gaj\| PDB=3gaj \| SCENE= }}		{{STRUCTURE_3gaj\| PDB=3gaj \| SCENE= }}

	===Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP===		===Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19236001}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19236001 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19236001}}		{{ABSTRACT_PUBMED_19236001}}

	==About this Structure==		==About this Structure==
-	~~3GAJ~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_reuteri Lactobacillus reuteri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA].	+	[[3gaj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_reuteri Lactobacillus reuteri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19236001~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019236001</ref><references group="xtra"/>
	[[Category: Lactobacillus reuteri]]		[[Category: Lactobacillus reuteri]]
	[[Category: Escalante-Semerena, J C.]]		[[Category: Escalante-Semerena, J C.]]
Line 30:		Line 18:
	[[Category: Rayment, I.]]		[[Category: Rayment, I.]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 8 09:28:45 2009''

OCA at 06:28, 8 July 2009

OCA — Wed, 08 Jul 2009 06:28:47 GMT

←Older revision		Revision as of 06:28, 8 July 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3gaj.jpg\|left\|200px]]

-	The ~~entry 3gaj~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3gaj", 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_3gaj\| PDB=3gaj \| SCENE= }}

-	~~Authors: St Maurice, M., Mera, P.E., Escalante-Semerena, J.~~C~~., Rayment, I.~~	+	===Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP===

-	Description: Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar~~ ~~4 14~~:46:00 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19236001}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19236001 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19236001}}
		+
		+	==About this Structure==
		+	3GAJ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Lactobacillus_reuteri Lactobacillus reuteri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GAJ OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19236001</ref><references group="xtra"/>
		+	[[Category: Lactobacillus reuteri]]
		+	[[Category: Escalante-Semerena, J C.]]
		+	[[Category: Maurice, M St.]]
		+	[[Category: Mera, P E.]]
		+	[[Category: Rayment, I.]]
		+	[[Category: Transferase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 8 09:28:45 2009''

OCA: New page: '''Unreleased structure''' The entry 3gaj is ON HOLD Authors: St Maurice, M., Mera, P.E., Escalante-Semerena, J.C., Rayment, I. Description: Structure of a C-terminal deletion variant ...

OCA — Wed, 04 Mar 2009 12:46:01 GMT

New page: '''Unreleased structure''' The entry 3gaj is ON HOLD Authors: St Maurice, M., Mera, P.E., Escalante-Semerena, J.C., Rayment, I. Description: Structure of a C-terminal deletion variant ...

New page

'''Unreleased structure'''

The entry 3gaj is ON HOLD

Authors: St Maurice, M., Mera, P.E., Escalante-Semerena, J.C., Rayment, I.

Description: Structure of a C-terminal deletion variant of a PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 4 14:46:00 2009''