2ptr - Revision history

OCA at 09:11, 21 February 2024

2024-02-21T09:11:54Z

← Older revision		Revision as of 09:11, 21 February 2024
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	<StructureSection load='2ptr' size='340' side='right'caption='[[2ptr]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2ptr' size='340' side='right'caption='[[2ptr]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ptr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ptr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PTR FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=2SA:2~~-~~[9-(3~~,~~4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC+ACID'>2SA</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]] 1.85Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em~~;~~'>[[2ptq\|2ptq]], [[2pts\|2pts]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2SA:2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC+ACID'>2SA</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>purB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~https://en.wikipedia.org/wiki/Adenylosuccinate_lyase Adenylosuccinate lyase], with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=4.~~3~~.2.2~~ 4~~.3.2.~~2] </~~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=2ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptr OCA], [https://pdbe.org/2ptr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ptr RCSB], [https://www.ebi.ac.uk/pdbsum/2ptr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ptr 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=2ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptr OCA], [https://pdbe.org/2ptr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ptr RCSB], [https://www.ebi.ac.uk/pdbsum/2ptr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ptr ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/PUR8_ECOLI PUR8_ECOLI]
	== 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=2ptr 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=2ptr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Adenylosuccinate lyase (ADL) catalyzes the breakdown of 5-aminoimidazole- (N-succinylocarboxamide) ribotide (SAICAR) to 5-aminoimidazole-4-carboxamide ribotide (AICAR) and fumarate, and of adenylosuccinate (ADS) to adenosine monophosphate (AMP) and fumarate in the de novo purine biosynthetic pathway. ADL belongs to the argininosuccinate lyase (ASL)/fumarase C superfamily of enzymes. Members of this family share several common features including: a mainly alpha-helical, homotetrameric structure; three regions of highly conserved amino acid residues; and a general acid-base catalytic mechanism with the overall beta-elimination of fumarate as a product. The crystal structures of wild-type Escherichia coli ADL (ec-ADL), and mutant-substrate (H171A-ADS) and -product (H171N-AMP.FUM) complexes have been determined to 2.0, 1.85, and 2.0 A resolution, respectively. The H171A-ADS and H171N-AMP.FUM structures provide the first detailed picture of the ADL active site, and have enabled the precise identification of substrate binding and putative catalytic residues. Contrary to previous suggestions, the ec-ADL structures implicate S295 and H171 in base and acid catalysis, respectively. Furthermore, structural alignments of ec-ADL with other superfamily members suggest for the first time a large conformational movement of the flexible C3 loop (residues 287-303) in ec-ADL upon substrate binding and catalysis, resulting in its closure over the active site. This loop movement has been observed in other superfamily enzymes, and has been proposed to be essential for catalysis. The ADL catalytic mechanism is re-examined in light of the results presented here.

	Substrate and product complexes of Escherichia coli adenylosuccinate lyase provide new insights into the enzymatic mechanism.,Tsai M, Koo J, Yip P, Colman RF, Segall ML, Howell PL J Mol Biol. 2007 Jul 13;370(3):541-54. Epub 2007 May 4. PMID:17531264<ref>PMID:17531264</ref>

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

	==See Also==		==See Also==
	*[[Adenylosuccinate lyase 3D structures\|Adenylosuccinate lyase 3D structures]]		*[[Adenylosuccinate lyase 3D structures\|Adenylosuccinate lyase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~		[[Category: Escherichia coli]]
	~~[[Category: Adenylosuccinate lyase~~]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Howell~~, P L~~]]		[[Category: Howell PL]]
	[[Category: Tsai, M]]		[[Category: Tsai M]]
	~~[[Category: Lyase]]~~
	~~[[Category: Mutant-substrate complex~~]]

OCA at 15:32, 17 June 2021

2021-06-17T15:32:40Z

← Older revision		Revision as of 15:32, 17 June 2021
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	==Crystal structure of Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate==		==Crystal structure of Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate==
	<StructureSection load='2ptr' size='340' side='right' caption='[[2ptr]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2ptr' size='340' side='right'caption='[[2ptr]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ptr]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PTR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ptr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PTR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PTR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2SA:2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC+ACID'>2SA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2SA:2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC+ACID'>2SA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ptq\|2ptq]], [[2pts\|2pts]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ptq\|2ptq]], [[2pts\|2pts]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">purB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">purB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Adenylosuccinate_lyase Adenylosuccinate lyase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.2.2 4.3.2.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Adenylosuccinate_lyase Adenylosuccinate lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.2.2 4.3.2.2] </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=2ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptr OCA], [~~http~~://pdbe.org/2ptr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ptr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ptr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ptr 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=2ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptr OCA], [https://pdbe.org/2ptr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ptr RCSB], [https://www.ebi.ac.uk/pdbsum/2ptr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ptr ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
	*[[Adenylosuccinate lyase\|Adenylosuccinate lyase]]		*[[Adenylosuccinate lyase 3D structures\|Adenylosuccinate lyase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 38:		Line 38:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Adenylosuccinate lyase]]		[[Category: Adenylosuccinate lyase]]
			[[Category: Large Structures]]
	[[Category: Howell, P L]]		[[Category: Howell, P L]]
	[[Category: Tsai, M]]		[[Category: Tsai, M]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Mutant-substrate complex]]		[[Category: Mutant-substrate complex]]

OCA at 08:50, 29 August 2018

2018-08-29T08:50:29Z

← Older revision		Revision as of 08:50, 29 August 2018
Line 1:		Line 1:

	==Crystal structure of Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate==		==Crystal structure of Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate==
	<StructureSection load='2ptr' size='340' side='right' caption='[[2ptr]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2ptr' size='340' side='right' caption='[[2ptr]], [[Resolution\|resolution]] 1.85Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">purB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">purB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylosuccinate_lyase Adenylosuccinate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.2.2 4.3.2.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylosuccinate_lyase Adenylosuccinate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.2.2 4.3.2.2] </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=2ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptr OCA], [http://pdbe.org/2ptr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ptr RCSB], [http://www.ebi.ac.uk/pdbsum/2ptr 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=2ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptr OCA], [http://pdbe.org/2ptr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ptr RCSB], [http://www.ebi.ac.uk/pdbsum/2ptr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ptr ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pt/2ptr_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pt/2ptr_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>
	</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=2ptr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 2ptr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2ptr" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Adenylosuccinate lyase\|Adenylosuccinate lyase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:01, 11 September 2015

2015-09-11T14:01:15Z

← Older revision		Revision as of 14:01, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2ptr' size='340' side='right' caption='[[2ptr]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='2ptr' size='340' side='right' caption='[[2ptr]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ptr]] is a 2 chain structure with sequence 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=2PTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ptr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PTR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2SA:2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC+ACID'>2SA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2SA:2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC+ACID'>2SA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ptq\|2ptq]], [[2pts\|2pts]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ptq\|2ptq]], [[2pts\|2pts]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">purB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">purB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylosuccinate_lyase Adenylosuccinate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.2.2 4.3.2.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylosuccinate_lyase Adenylosuccinate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.2.2 4.3.2.2] </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=2ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ptr RCSB], [http://www.ebi.ac.uk/pdbsum/2ptr 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=2ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptr OCA], [http://pdbe.org/2ptr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ptr RCSB], [http://www.ebi.ac.uk/pdbsum/2ptr PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 2ptr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Bacillus coli migula 1895]]
	[[Category: Adenylosuccinate lyase]]		[[Category: Adenylosuccinate lyase]]
	~~[[Category: Escherichia coli]]~~
	[[Category: Howell, P L]]		[[Category: Howell, P L]]
	[[Category: Tsai, M]]		[[Category: Tsai, M]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Mutant-substrate complex]]		[[Category: Mutant-substrate complex]]

OCA at 14:10, 19 January 2015

2015-01-19T14:10:36Z

← Older revision		Revision as of 14:10, 19 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ptr]] is a 2 chain structure with sequence 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=2PTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PTR FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ptr]] is a 2 chain structure with sequence 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=2PTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PTR FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2SA:2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC+ACID'>2SA</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2SA:2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC+ACID'>2SA</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ptq\|2ptq]], [[2pts\|2pts]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ptq\|2ptq]], [[2pts\|2pts]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">purB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">purB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylosuccinate_lyase Adenylosuccinate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.2.2 4.3.2.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylosuccinate_lyase Adenylosuccinate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.2.2 4.3.2.2] </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=2ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ptr RCSB], [http://www.ebi.ac.uk/pdbsum/2ptr 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=2ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ptr RCSB], [http://www.ebi.ac.uk/pdbsum/2ptr 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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	[[Category: Adenylosuccinate lyase]]		[[Category: Adenylosuccinate lyase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Howell, P L.]]		[[Category: Howell, P L]]
	[[Category: Tsai, M~~.]]~~		[[Category: Tsai, M]]
	~~[[Category: Adenylosuccinate lyase~~]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Mutant-substrate complex]]		[[Category: Mutant-substrate complex]]

OCA at 18:24, 30 September 2014

2014-09-30T18:24:13Z

← Older revision		Revision as of 18:24, 30 September 2014
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	[[Image:~~2ptr~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate==
			<StructureSection load='2ptr' size='340' side='right' caption='[[2ptr]], [[Resolution\|resolution]] 1.85Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2ptr]] is a 2 chain structure with sequence 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=2PTR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PTR FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2SA:2-[9-(3,4-DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-9H-PURIN-6-YLAMINO]-SUCCINIC+ACID'>2SA</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ptq\|2ptq]], [[2pts\|2pts]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">purB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenylosuccinate_lyase Adenylosuccinate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.2.2 4.3.2.2] </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=2ptr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ptr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ptr RCSB], [http://www.ebi.ac.uk/pdbsum/2ptr 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/pt/2ptr_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 ==
			Adenylosuccinate lyase (ADL) catalyzes the breakdown of 5-aminoimidazole- (N-succinylocarboxamide) ribotide (SAICAR) to 5-aminoimidazole-4-carboxamide ribotide (AICAR) and fumarate, and of adenylosuccinate (ADS) to adenosine monophosphate (AMP) and fumarate in the de novo purine biosynthetic pathway. ADL belongs to the argininosuccinate lyase (ASL)/fumarase C superfamily of enzymes. Members of this family share several common features including: a mainly alpha-helical, homotetrameric structure; three regions of highly conserved amino acid residues; and a general acid-base catalytic mechanism with the overall beta-elimination of fumarate as a product. The crystal structures of wild-type Escherichia coli ADL (ec-ADL), and mutant-substrate (H171A-ADS) and -product (H171N-AMP.FUM) complexes have been determined to 2.0, 1.85, and 2.0 A resolution, respectively. The H171A-ADS and H171N-AMP.FUM structures provide the first detailed picture of the ADL active site, and have enabled the precise identification of substrate binding and putative catalytic residues. Contrary to previous suggestions, the ec-ADL structures implicate S295 and H171 in base and acid catalysis, respectively. Furthermore, structural alignments of ec-ADL with other superfamily members suggest for the first time a large conformational movement of the flexible C3 loop (residues 287-303) in ec-ADL upon substrate binding and catalysis, resulting in its closure over the active site. This loop movement has been observed in other superfamily enzymes, and has been proposed to be essential for catalysis. The ADL catalytic mechanism is re-examined in light of the results presented here.

	~~{{STRUCTURE_2ptr\| PDB=2ptr \| SCENE= }}~~		Substrate and product complexes of Escherichia coli adenylosuccinate lyase provide new insights into the enzymatic mechanism.,Tsai M, Koo J, Yip P, Colman RF, Segall ML, Howell PL J Mol Biol. 2007 Jul 13;370(3):541-54. Epub 2007 May 4. PMID:17531264<ref>PMID:17531264</ref>

	~~===Crystal structure~~ of ~~Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17531264}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2ptr]] is a 2 chain structure with sequence 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=2PTR OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017531264<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Adenylosuccinate lyase]]		[[Category: Adenylosuccinate lyase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

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

2013-01-07T13:15:28Z

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

← Older revision	Revision as of 13:15, 7 January 2013
(No difference)

OCA at 13:15, 7 January 2013

2013-01-07T13:15:25Z

← Older revision		Revision as of 13:15, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2ptr.png\|left\|200px]]		[[Image:2ptr.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2ptr", 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_2ptr\| PDB=2ptr \| SCENE= }}		{{STRUCTURE_2ptr\| PDB=2ptr \| SCENE= }}

	===Crystal structure of Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate===		===Crystal structure of Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17531264}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17531264 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17531264}}		{{ABSTRACT_PUBMED_17531264}}

	==About this Structure==		==About this Structure==
	~~2PTR~~ 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=2PTR OCA].		[[2ptr]] is a 2 chain structure with sequence 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=2PTR OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17531264~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017531264</ref><references group="xtra"/>
	[[Category: Adenylosuccinate lyase]]		[[Category: Adenylosuccinate lyase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
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	[[Category: Tsai, M.]]		[[Category: Tsai, M.]]
	[[Category: Adenylosuccinate lyase]]		[[Category: Adenylosuccinate lyase]]
			[[Category: Lyase]]
	[[Category: Mutant-substrate complex]]		[[Category: Mutant-substrate complex]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:09:39 2009''~~

OCA at 22:09, 17 February 2009

2009-02-17T22:09:41Z

← Older revision		Revision as of 22:09, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2PTR is a ~~[[Single protein]]~~ structure of ~~sequence~~ 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=2PTR OCA].		2PTR 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=2PTR OCA].

	==Reference==		==Reference==
	Substrate and product complexes of Escherichia coli adenylosuccinate lyase provide new insights into the enzymatic mechanism., Tsai M, Koo J, Yip P, Colman RF, Segall ML, Howell PL, J Mol Biol. 2007 Jul 13;370(3):541-54. Epub 2007 May 4. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17531264 17531264]~~		<ref group="xtra">PMID:17531264</ref><references group="xtra"/>
	[[Category: Adenylosuccinate lyase]]		[[Category: Adenylosuccinate lyase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	~~[[Category: Single protein]]~~
	[[Category: Howell, P L.]]		[[Category: Howell, P L.]]
	[[Category: Tsai, M.]]		[[Category: Tsai, M.]]
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	[[Category: Mutant-substrate complex]]		[[Category: Mutant-substrate complex]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 07~~:29:~~20 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:09:39 2009''

OCA at 04:29, 29 July 2008

2008-07-29T04:29:26Z

← Older revision		Revision as of 04:29, 29 July 2008
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	[[Image:2ptr.~~jpg~~\|left\|200px]]		{{Seed}}
			[[Image:2ptr.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2ptr\| PDB=2ptr \| SCENE= }}		{{STRUCTURE_2ptr\| PDB=2ptr \| SCENE= }}

	~~'''~~Crystal structure of Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate~~'''~~		===Crystal structure of Escherichia coli adenylosuccinate lyase mutant H171A with bound adenylosuccinate substrate===


	~~==Overview==~~		<!--
	~~Adenylosuccinate lyase (ADL) catalyzes the breakdown of 5~~-~~aminoimidazole~~- ~~(N-succinylocarboxamide) ribotide (SAICAR) to 5-aminoimidazole-4-carboxamide ribotide (AICAR) and fumarate~~, ~~and of adenylosuccinate (ADS) to adenosine monophosphate (AMP) and fumarate in~~ the ~~de novo purine biosynthetic pathway. ADL belongs~~ to the ~~argininosuccinate lyase~~ (~~ASL)~~/~~fumarase C superfamily of enzymes~~. Members of this family share several common features including: a mainly alpha-helical, homotetrameric structure; three regions of highly conserved amino acid residues; and a general acid-base catalytic mechanism with the overall beta-elimination of fumarate as a product. ~~The crystal structures of wild-type Escherichia coli ADL (ec-ADL~~), ~~and mutant-substrate (H171A-ADS) and -product (H171N-AMP.FUM) complexes have been determined to 2.0, 1.85, and 2.0 A resolution, respectively. The H171A-ADS and H171N-AMP.FUM structures provide~~ the ~~first detailed picture of the ADL active site, and have enabled the precise identification of substrate binding and putative catalytic residues~~. ~~Contrary to previous suggestions, the ec~~-~~ADL structures implicate S295 and H171 in base and acid catalysis, respectively. Furthermore, structural alignments of ec~~-ADL with other superfamily members suggest for the first time a large conformational movement of the flexible C3 loop (residues 287-303) in ec-ADL upon substrate binding and catalysis, resulting in its closure over the active site. This loop movement has been observed in other superfamily enzymes, and has been proposed to be essential for catalysis. The ADL catalytic mechanism is re-examined in light of the results presented here.		The line below this paragraph, {{ABSTRACT_PUBMED_17531264}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 17531264 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_17531264}}

	==About this Structure==		==About this Structure==
Line 27:		Line 31:
	[[Category: Adenylosuccinate lyase]]		[[Category: Adenylosuccinate lyase]]
	[[Category: Mutant-substrate complex]]		[[Category: Mutant-substrate complex]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 13~~:47:23 2008''
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 07:29:20 2008''