2imo - Revision history

OCA at 07:40, 9 October 2024

2024-10-09T07:40:13Z

← Older revision		Revision as of 07:40, 9 October 2024
Line 1:		Line 1:

	==Crystal structure of allantoate amidohydrolase from Escherichia coli at pH 4.6==		==Crystal structure of allantoate amidohydrolase from Escherichia coli at pH 4.6==
	<StructureSection load='2imo' size='340' side='right'caption='[[2imo]]' scene=''>		<StructureSection load='2imo' size='340' side='right'caption='[[2imo]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IMO FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IMO FirstGlance]. <br>
	</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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [https://pdbe.org/2imo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [https://www.ebi.ac.uk/pdbsum/2imo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2imo ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</span></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]] 2.8Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [https://pdbe.org/2imo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [https://www.ebi.ac.uk/pdbsum/2imo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2imo ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 11:		Line 13:
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/im/2imo_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/im/2imo_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/~~initialview01~~.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
	<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/main_output.php?pdb_ID=2imo 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=2imo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Purine metabolism plays a major role in regulating the availability of purine nucleotides destined for nucleic acid synthesis. Allantoate amidohydrolase catalyzes the conversion of allantoate to (S)-ureidoglycolate, one of the crucial alternate steps in purine metabolism. The crystal structure of a ternary complex of allantoate amidohydrolase with its substrate allantoate and an allosteric effector, a sulfate ion, from Escherichia coli was determined to understand better the catalytic mechanism and substrate specificity. The 2.25 A resolution X-ray structure reveals an alpha/beta scaffold akin to zinc exopeptidases of the peptidase M20 family and lacks the (beta/alpha)(8)-barrel fold characteristic of the amidohydrolases. Arrangement of the substrate and the two co-catalytic zinc ions at the active site governs catalytic specificity for hydrolysis of N-carbamyl versus the peptide bond in exopeptidases. In its crystalline form, allantoate amidohydrolase adopts a relatively open conformation. However, structural analysis reveals the possibility of a significant movement of domains via rotation about two hinge regions upon allosteric effector and substrate binding resulting in a closed catalytically competent conformation by bringing the substrate allantoate closer to co-catalytic zinc ions. Two cis-prolyl peptide bonds found on either side of the dimerization domain in close proximity to the substrate and ligand-binding sites may be involved in protein folding and in preserving the integrity of the catalytic site.

			Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics.,Agarwal R, Burley SK, Swaminathan S J Mol Biol. 2007 Apr 27;368(2):450-63. Epub 2007 Feb 20. PMID:17362992<ref>PMID:17362992</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 2imo" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:19, 31 March 2021

2021-03-31T11:19:02Z

← Older revision		Revision as of 11:19, 31 March 2021
Line 1:		Line 1:

	==Crystal structure of allantoate amidohydrolase from Escherichia coli at pH 4.6==		==Crystal structure of allantoate amidohydrolase from Escherichia coli at pH 4.6==
	<StructureSection load='2imo' size='340' side='right' caption='[[2imo]]~~, [[Resolution\|resolution]] 2.80Å~~' scene=''>		<StructureSection load='2imo' size='340' side='right'caption='[[2imo]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>~~[[2imo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2IMO FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IMO FirstGlance]. <br>
	</td></tr>~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>~~		</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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [https://pdbe.org/2imo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [https://www.ebi.ac.uk/pdbsum/2imo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2imo ProSAT], [https://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</span></td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z2l\|1z2l]]</td></tr>~~
	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">allC_ecoli ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [~~http~~://pdbe.org/2imo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2imo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2imo ProSAT], [~~http~~://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</span></td></tr>
	</table>		</table>
	~~== Function ==~~
	~~[[http://www.uniprot.org/uniprot/ALLC_ECOLI ALLC_ECOLI]] Involved in the anaerobic utilization of allantoin. Converts allantoate to (S)-ureidoglycolate and ammonia.<ref>PMID:10601204</ref>~~
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 16:
	</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=2imo 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=2imo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Purine metabolism plays a major role in regulating the availability of purine nucleotides destined for nucleic acid synthesis. Allantoate amidohydrolase catalyzes the conversion of allantoate to (S)-ureidoglycolate, one of the crucial alternate steps in purine metabolism. The crystal structure of a ternary complex of allantoate amidohydrolase with its substrate allantoate and an allosteric effector, a sulfate ion, from Escherichia coli was determined to understand better the catalytic mechanism and substrate specificity. The 2.25 A resolution X-ray structure reveals an alpha/beta scaffold akin to zinc exopeptidases of the peptidase M20 family and lacks the (beta/alpha)(8)-barrel fold characteristic of the amidohydrolases. Arrangement of the substrate and the two co-catalytic zinc ions at the active site governs catalytic specificity for hydrolysis of N-carbamyl versus the peptide bond in exopeptidases. In its crystalline form, allantoate amidohydrolase adopts a relatively open conformation. However, structural analysis reveals the possibility of a significant movement of domains via rotation about two hinge regions upon allosteric effector and substrate binding resulting in a closed catalytically competent conformation by bringing the substrate allantoate closer to co-catalytic zinc ions. Two cis-prolyl peptide bonds found on either side of the dimerization domain in close proximity to the substrate and ligand-binding sites may be involved in protein folding and in preserving the integrity of the catalytic site.

	Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics.,Agarwal R, Burley SK, Swaminathan S J Mol Biol. 2007 Apr 27;368(2):450-63. Epub 2007 Feb 20. PMID:17362992<ref>PMID:17362992</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2imo" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Ecoli~~]]		[[Category: Large Structures]]
	[[Category: Agarwal, R]]		[[Category: Agarwal R]]
	[[Category: Burley~~, S K]]~~		[[Category: Burley SK]]
	~~[[Category: Structural genomic~~]]		[[Category: Swaminathan S]]
	[[Category: Swaminathan, S]]
	~~[[Category: Allantoate amidohydrolase]]~~
	~~[[Category: Allc]]~~
	~~[[Category: Apoenzyme]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]~~
	~~[[Category: PSI, Protein structure initiative]]~~
	~~[[Category: T1507~~]]

OCA at 08:30, 4 July 2018

2018-07-04T08:30:10Z

← Older revision		Revision as of 08:30, 4 July 2018
Line 1:		Line 1:

	==Crystal structure of allantoate amidohydrolase from Escherichia coli at pH 4.6==		==Crystal structure of allantoate amidohydrolase from Escherichia coli at pH 4.6==
	<StructureSection load='2imo' size='340' side='right' caption='[[2imo]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2imo' size='340' side='right' caption='[[2imo]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z2l\|1z2l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z2l\|1z2l]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">allC_ecoli ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">allC_ecoli ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [http://pdbe.org/2imo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [http://www.ebi.ac.uk/pdbsum/2imo PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [http://pdbe.org/2imo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [http://www.ebi.ac.uk/pdbsum/2imo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2imo ProSAT], [http://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/im/2imo_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/im/2imo_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 02:02, 10 February 2016

2016-02-10T02:02:00Z

← Older revision		Revision as of 02:02, 10 February 2016
Line 18:		Line 18:
	<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=2imo ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 04:16, 11 September 2015

2015-09-11T04:16:38Z

← Older revision		Revision as of 04:16, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2imo' size='340' side='right' caption='[[2imo]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='2imo' size='340' side='right' caption='[[2imo]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2imo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IMO FirstGlance]. <br>		<table><tr><td colspan='2'>[[2imo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IMO FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z2l\|1z2l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z2l\|1z2l]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">allC_ecoli ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ~~Escherichia coli K-12~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">allC_ecoli ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [http://www.ebi.ac.uk/pdbsum/2imo PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [http://pdbe.org/2imo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [http://www.ebi.ac.uk/pdbsum/2imo PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 2imo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Escherichia coli k-12~~]]		[[Category: Ecoli]]
	[[Category: Agarwal, R]]		[[Category: Agarwal, R]]
	[[Category: Burley, S K]]		[[Category: Burley, S K]]

OCA at 11:01, 25 December 2014

2014-12-25T11:01:27Z

← Older revision		Revision as of 11:01, 25 December 2014
Line 8:		Line 8:
	<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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [http://www.ebi.ac.uk/pdbsum/2imo PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [http://www.ebi.ac.uk/pdbsum/2imo PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/ALLC_ECOLI ALLC_ECOLI]] Involved in the anaerobic utilization of allantoin. Converts allantoate to (S)-ureidoglycolate and ammonia.<ref>PMID:10601204</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 13:47, 6 November 2014

2014-11-06T13:47:00Z

← Older revision		Revision as of 13:47, 6 November 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2imo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IMO FirstGlance]. <br>		<table><tr><td colspan='2'>[[2imo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IMO FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z2l\|1z2l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z2l\|1z2l]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">allC_ecoli ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">allC_ecoli ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [http://www.ebi.ac.uk/pdbsum/2imo PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [http://www.ebi.ac.uk/pdbsum/2imo PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</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: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Agarwal, R.]]		[[Category: Agarwal, R]]
	[[Category: Burley, S K.]]		[[Category: Burley, S K]]
	[[Category: ~~NYSGXRC, New York SGX Research Center for~~ Structural ~~Genomics.~~]]		[[Category: Structural genomic]]
	[[Category: Swaminathan, S.]]		[[Category: Swaminathan, S]]
	[[Category: Allantoate amidohydrolase]]		[[Category: Allantoate amidohydrolase]]
	[[Category: Allc]]		[[Category: Allc]]
	[[Category: Apoenzyme]]		[[Category: Apoenzyme]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: New ~~york sgx research center~~ for ~~structural genomic]]~~		[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics]]
	~~[[Category: Nysgxrc~~]]		[[Category: PSI, Protein structure initiative]]
	[[Category: Protein structure initiative]]
	~~[[Category: Psi-2]]~~
	~~[[Category: Structural genomic~~]]
	[[Category: T1507]]		[[Category: T1507]]

OCA at 10:50, 30 September 2014

2014-09-30T10:50:07Z

← Older revision		Revision as of 10:50, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2imo~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of allantoate amidohydrolase from Escherichia coli at pH 4.6==
			<StructureSection load='2imo' size='340' side='right' caption='[[2imo]], [[Resolution\|resolution]] 2.80Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2imo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2IMO FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1z2l\|1z2l]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">allC_ecoli ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 Escherichia coli K-12])</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=2imo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2imo OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2imo RCSB], [http://www.ebi.ac.uk/pdbsum/2imo PDBsum], [http://www.topsan.org/Proteins/NYSGXRC/2imo TOPSAN]</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/im/2imo_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 ==
			Purine metabolism plays a major role in regulating the availability of purine nucleotides destined for nucleic acid synthesis. Allantoate amidohydrolase catalyzes the conversion of allantoate to (S)-ureidoglycolate, one of the crucial alternate steps in purine metabolism. The crystal structure of a ternary complex of allantoate amidohydrolase with its substrate allantoate and an allosteric effector, a sulfate ion, from Escherichia coli was determined to understand better the catalytic mechanism and substrate specificity. The 2.25 A resolution X-ray structure reveals an alpha/beta scaffold akin to zinc exopeptidases of the peptidase M20 family and lacks the (beta/alpha)(8)-barrel fold characteristic of the amidohydrolases. Arrangement of the substrate and the two co-catalytic zinc ions at the active site governs catalytic specificity for hydrolysis of N-carbamyl versus the peptide bond in exopeptidases. In its crystalline form, allantoate amidohydrolase adopts a relatively open conformation. However, structural analysis reveals the possibility of a significant movement of domains via rotation about two hinge regions upon allosteric effector and substrate binding resulting in a closed catalytically competent conformation by bringing the substrate allantoate closer to co-catalytic zinc ions. Two cis-prolyl peptide bonds found on either side of the dimerization domain in close proximity to the substrate and ligand-binding sites may be involved in protein folding and in preserving the integrity of the catalytic site.

	~~{{STRUCTURE_2imo\| PDB=2imo \| SCENE= }}~~		Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics.,Agarwal R, Burley SK, Swaminathan S J Mol Biol. 2007 Apr 27;368(2):450-63. Epub 2007 Feb 20. PMID:17362992<ref>PMID:17362992</ref>

	~~===Crystal structure~~ of ~~allantoate amidohydrolase from Escherichia coli at pH 4~~.~~6===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17362992}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2imo]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org~~/~~wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMO OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017362992<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Escherichia coli k-12]]		[[Category: Escherichia coli k-12]]
	[[Category: Agarwal, R.]]		[[Category: Agarwal, R.]]

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

2013-01-07T15:18:40Z

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

← Older revision	Revision as of 15:18, 7 January 2013
(No difference)

OCA at 15:18, 7 January 2013

2013-01-07T15:18:37Z

← Older revision		Revision as of 15:18, 7 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:2imo.png\|left\|200px]]		[[Image:2imo.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2imo", 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_2imo\| PDB=2imo \| SCENE= }}		{{STRUCTURE_2imo\| PDB=2imo \| SCENE= }}

	===Crystal structure of allantoate amidohydrolase from Escherichia coli at pH 4.6===		===Crystal structure of allantoate amidohydrolase from Escherichia coli at pH 4.6===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17362992}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17362992 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17362992}}		{{ABSTRACT_PUBMED_17362992}}

	==About this Structure==		==About this Structure==
	~~2IMO~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Escherichia_coli~~ Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMO OCA].		[[2imo]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IMO OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17362992~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017362992</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli k-12]]
	[[Category: Agarwal, R.]]		[[Category: Agarwal, R.]]
	[[Category: Burley, S K.]]		[[Category: Burley, S K.]]
	[[Category: NYSGXRC, New York Structural ~~GenomiX Research Consortium~~.]]		[[Category: NYSGXRC, New York SGX Research Center for Structural Genomics.]]
	[[Category: Swaminathan, S.]]		[[Category: Swaminathan, S.]]
	[[Category: Allantoate amidohydrolase]]		[[Category: Allantoate amidohydrolase]]
	[[Category: Allc]]		[[Category: Allc]]
	[[Category: Apoenzyme]]		[[Category: Apoenzyme]]
	[[Category: New york structural ~~genomix research consortium~~]]		[[Category: Hydrolase]]
			[[Category: New york sgx research center for structural genomic]]
	[[Category: Nysgxrc]]		[[Category: Nysgxrc]]
	[[Category: Protein structure initiative]]		[[Category: Protein structure initiative]]
Line 38:		Line 27:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: T1507]]		[[Category: T1507]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 14:31:31 2009''~~