3ci1 - Revision history

OCA at 09:35, 21 February 2024

OCA — Wed, 21 Feb 2024 09:35:48 GMT

←Older revision		Revision as of 09:35, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3ci1' size='340' side='right'caption='[[3ci1]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3ci1' size='340' side='right'caption='[[3ci1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ci1]] 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=3CI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CI1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ci1]] 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=3CI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CI1 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]] 1.9Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2nt8\|2nt8]], [[3ci3\|3ci3]], [[3ci4\|3ci4]]~~</~~div~~><~~/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 ([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~~'>[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=3ci1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ci1 OCA], [https://pdbe.org/3ci1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ci1 RCSB], [https://www.ebi.ac.uk/pdbsum/3ci1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ci1 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=3ci1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ci1 OCA], [https://pdbe.org/3ci1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ci1 RCSB], [https://www.ebi.ac.uk/pdbsum/3ci1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ci1 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=3ci1 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=3ci1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	ATP:cob(I)alamin adenosyltransferases (ACAs) catalyze the transfer of the 5'-deoxyadenosyl moiety from ATP to the upper axial ligand position of cobalamin in the synthesis of coenzyme B 12. For the ACA-catalyzed reaction to proceed, cob(II)alamin must be reduced to cob(I)alamin in the enzyme active site. This reduction is facilitated through the generation of a four-coordinate cob(II)alamin intermediate on the enzyme. We have determined the high-resolution crystal structure of a human-type ACA from Lactobacillus reuteri with a four-coordinate cob(II)alamin bound in the enzyme active site and with the product, adenosylcobalamin, partially occupied in the active site. The assembled structures represent snapshots of the steps in the ACA-catalyzed formation of the cobalt-carbon bond of coenzyme B 12. The structures define the corrinoid binding site and provide visual evidence for a base-off, four-coordinate cob(II)alamin intermediate. The complete structural description of ACA-mediated catalysis reveals the molecular features of four-coordinate cob(II)alamin stabilization and provides additional insights into the molecular basis for dysfunction in human patients suffering from methylmalonic aciduria.
-
-	Structural characterization of a human-type corrinoid adenosyltransferase confirms that coenzyme B12 is synthesized through a four-coordinate intermediate.,St Maurice M, Mera P, Park K, Brunold TC, Escalante-Semerena JC, Rayment I Biochemistry. 2008 May 27;47(21):5755-66. Epub 2008 May 2. PMID:18452306<ref>PMID:18452306</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3ci1" 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: Maurice MSt]]
-	[[Category: Rayment, I]]	+	[[Category: Mera PE]]
-	~~[[Category: Adenosyltransferase]]~~	+	[[Category: Rayment I]]
-	~~[[Category: Atp binding]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:56, 27 January 2022

OCA — Thu, 27 Jan 2022 07:56:34 GMT

←Older revision		Revision as of 07:56, 27 January 2022
Line 1:		Line 1:

	==Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)alamin and ATP==		==Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)alamin and ATP==
-	<StructureSection load='3ci1' size='340' side='right' caption='[[3ci1]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='3ci1' size='340' side='right'caption='[[3ci1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ci1]] 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=3CI1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3CI1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ci1]] 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=3CI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CI1 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nt8\|2nt8]], [[3ci3\|3ci3]], [[3ci4\|3ci4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2nt8\|2nt8]], [[3ci3\|3ci3]], [[3ci4\|3ci4]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA ([~~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 ([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=3ci1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ci1 OCA], [~~http~~://pdbe.org/3ci1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ci1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ci1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ci1 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=3ci1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ci1 OCA], [https://pdbe.org/3ci1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ci1 RCSB], [https://www.ebi.ac.uk/pdbsum/3ci1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ci1 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 34:		Line 34:
	</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 13:17, 7 November 2018

OCA — Wed, 07 Nov 2018 13:17:06 GMT

←Older revision		Revision as of 13:17, 7 November 2018
Line 1:		Line 1:
		+
	==Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)alamin and ATP==		==Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)alamin and ATP==
	<StructureSection load='3ci1' size='340' side='right' caption='[[3ci1]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3ci1' size='340' side='right' caption='[[3ci1]], [[Resolution\|resolution]] 1.90Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA ([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 ([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=3ci1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ci1 OCA], [http://pdbe.org/3ci1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ci1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ci1 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=3ci1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ci1 OCA], [http://pdbe.org/3ci1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ci1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ci1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ci1 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ci/3ci1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ci/3ci1_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 08:18, 7 February 2016

OCA — Sun, 07 Feb 2016 08:18:53 GMT

←Older revision		Revision as of 08:18, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3ci1' size='340' side='right' caption='[[3ci1]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='3ci1' size='340' side='right' caption='[[3ci1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ci1]] 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=3CI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CI1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ci1]] 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=3CI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CI1 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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nt8\|2nt8]], [[3ci3\|3ci3]], [[3ci4\|3ci4]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nt8\|2nt8]], [[3ci3\|3ci3]], [[3ci4\|3ci4]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA ([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 ([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=3ci1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ci1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ci1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ci1 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=3ci1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ci1 OCA], [http://pdbe.org/3ci1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ci1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ci1 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		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=3ci1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		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 3ci1" 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 11:07, 20 January 2015

OCA — Tue, 20 Jan 2015 11:07:29 GMT

←Older revision		Revision as of 11:07, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ci1]] 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=3CI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CI1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ci1]] 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=3CI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CI1 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>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nt8\|2nt8]], [[3ci3\|3ci3]], [[3ci4\|3ci4]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nt8\|2nt8]], [[3ci3\|3ci3]], [[3ci4\|3ci4]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA ([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 ([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=3ci1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ci1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ci1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ci1 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=3ci1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ci1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ci1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ci1 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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: Adenosyltransferase]]		[[Category: Adenosyltransferase]]
	[[Category: Atp binding]]		[[Category: Atp binding]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 09:33, 29 September 2014

OCA — Mon, 29 Sep 2014 09:33:56 GMT

←Older revision		Revision as of 09:33, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3ci1.~~png~~\|~~left~~\|200px]]	+	==Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)alamin and ATP==
		+	<StructureSection load='3ci1' size='340' side='right' caption='[[3ci1]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ci1]] 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=3CI1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CI1 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>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2nt8\|2nt8]], [[3ci3\|3ci3]], [[3ci4\|3ci4]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cobA ([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=3ci1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ci1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ci1 RCSB], [http://www.ebi.ac.uk/pdbsum/3ci1 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/ci/3ci1_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:cob(I)alamin adenosyltransferases (ACAs) catalyze the transfer of the 5'-deoxyadenosyl moiety from ATP to the upper axial ligand position of cobalamin in the synthesis of coenzyme B 12. For the ACA-catalyzed reaction to proceed, cob(II)alamin must be reduced to cob(I)alamin in the enzyme active site. This reduction is facilitated through the generation of a four-coordinate cob(II)alamin intermediate on the enzyme. We have determined the high-resolution crystal structure of a human-type ACA from Lactobacillus reuteri with a four-coordinate cob(II)alamin bound in the enzyme active site and with the product, adenosylcobalamin, partially occupied in the active site. The assembled structures represent snapshots of the steps in the ACA-catalyzed formation of the cobalt-carbon bond of coenzyme B 12. The structures define the corrinoid binding site and provide visual evidence for a base-off, four-coordinate cob(II)alamin intermediate. The complete structural description of ACA-mediated catalysis reveals the molecular features of four-coordinate cob(II)alamin stabilization and provides additional insights into the molecular basis for dysfunction in human patients suffering from methylmalonic aciduria.

-	~~{{STRUCTURE_3ci1\| PDB=3ci1 \| SCENE= }}~~	+	Structural characterization of a human-type corrinoid adenosyltransferase confirms that coenzyme B12 is synthesized through a four-coordinate intermediate.,St Maurice M, Mera P, Park K, Brunold TC, Escalante-Semerena JC, Rayment I Biochemistry. 2008 May 27;47(21):5755-66. Epub 2008 May 2. PMID:18452306<ref>PMID:18452306</ref>

-	~~===Structure~~ of the ~~PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)alamin and ATP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18452306}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3ci1]] 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=3CI1 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018452306<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Lactobacillus reuteri]]		[[Category: Lactobacillus reuteri]]
	[[Category: Escalante-Semerena, J C.]]		[[Category: Escalante-Semerena, J C.]]

OCA: Protected "3ci1" [edit=sysop:move=sysop]

OCA — Wed, 24 Oct 2012 06:30:43 GMT

Protected "3ci1" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:30, 24 October 2012

OCA at 06:30, 24 October 2012

OCA — Wed, 24 Oct 2012 06:30:41 GMT

←Older revision		Revision as of 06:30, 24 October 2012
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-	{{Seed}}
	[[Image:3ci1.png\|left\|200px]]		[[Image:3ci1.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ci1", 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_3ci1\| PDB=3ci1 \| SCENE= }}		{{STRUCTURE_3ci1\| PDB=3ci1 \| SCENE= }}

	===Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)alamin and ATP===		===Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)alamin and ATP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18452306}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18452306 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18452306}}		{{ABSTRACT_PUBMED_18452306}}

	==About this Structure==		==About this Structure==
-	~~3CI1~~ 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=3CI1 OCA].	+	[[3ci1]] 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=3CI1 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18452306~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018452306</ref><references group="xtra"/>
	[[Category: Lactobacillus reuteri]]		[[Category: Lactobacillus reuteri]]
	[[Category: Escalante-Semerena, J C.]]		[[Category: Escalante-Semerena, J C.]]
Line 31:		Line 19:
	[[Category: Adenosyltransferase]]		[[Category: Adenosyltransferase]]
	[[Category: Atp binding]]		[[Category: Atp binding]]
-		+	[[Category: Transferase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 12:31:58 2009''~~	+

OCA at 10:31, 16 February 2009

OCA — Mon, 16 Feb 2009 10:31:59 GMT

←Older revision		Revision as of 10:31, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3CI1 is a ~~[[Single protein]]~~ 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=3CI1 OCA].	+	3CI1 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=3CI1 OCA].

	==Reference==		==Reference==
-	Structural characterization of a human-type corrinoid adenosyltransferase confirms that coenzyme B12 is synthesized through a four-coordinate intermediate., St Maurice M, Mera P, Park K, Brunold TC, Escalante-Semerena JC, Rayment I, Biochemistry. 2008 May 27;47(21):5755-66. Epub 2008 May 2. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18452306 18452306]~~	+	<ref group="xtra">PMID:18452306</ref><references group="xtra"/>
	[[Category: Lactobacillus reuteri]]		[[Category: Lactobacillus reuteri]]
-	[[Category: Single protein]]
	[[Category: Escalante-Semerena, J C.]]		[[Category: Escalante-Semerena, J C.]]
	[[Category: Maurice, M St.]]		[[Category: Maurice, M St.]]
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	[[Category: Atp binding]]		[[Category: Atp binding]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 14~~:46:~~22 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:31:58 2009''

OCA at 11:46, 27 July 2008

OCA — Sun, 27 Jul 2008 11:46:25 GMT

←Older revision		Revision as of 11:46, 27 July 2008
Line 1:		Line 1:
-	[[Image:3ci1.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:3ci1.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_3ci1\| PDB=3ci1 \| SCENE= }}		{{STRUCTURE_3ci1\| PDB=3ci1 \| SCENE= }}

-	~~'''~~Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)alamin and ATP~~'''~~	+	===Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)alamin and ATP===


-	~~==Overview==~~	+	<!--
-	~~ATP:cob(I)alamin adenosyltransferases (ACAs) catalyze the transfer of the 5'~~-~~deoxyadenosyl moiety from ATP to the upper axial ligand position of cobalamin in the synthesis of coenzyme B 12. For the ACA~~-~~catalyzed reaction to proceed~~, ~~cob(II)alamin must be reduced~~ to ~~cob(I)alamin in~~ the ~~enzyme active site. This reduction is facilitated through the generation of a four-coordinate cob~~(~~II)alamin intermediate~~ on ~~the enzyme~~. ~~We have determined the high-resolution crystal structure of a human-type ACA from Lactobacillus reuteri with a four-coordinate cob(II~~)~~alamin bound in the enzyme active site and with the product~~, ~~adenosylcobalamin, partially occupied in~~ the ~~active site~~. ~~The assembled structures represent snapshots of the steps in the ACA~~-~~catalyzed formation of the cobalt~~-carbon bond of coenzyme B 12. The structures define the corrinoid binding site and provide visual evidence for a base-off, four-coordinate cob(II)alamin intermediate. The complete structural description of ACA-mediated catalysis reveals the molecular features of four-coordinate cob(II)alamin stabilization and provides additional insights into the molecular basis for dysfunction in human patients suffering from methylmalonic aciduria.	+	The line below this paragraph, {{ABSTRACT_PUBMED_18452306}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18452306 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18452306}}

	==About this Structure==		==About this Structure==
Line 28:		Line 32:
	[[Category: Adenosyltransferase]]		[[Category: Adenosyltransferase]]
	[[Category: Atp binding]]		[[Category: Atp binding]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed May 28 09~~:22:19 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 14:46:22 2008''