1bq1 - Revision history

OCA at 15:35, 13 March 2024

OCA — Wed, 13 Mar 2024 15:35:15 GMT

←Older revision		Revision as of 15:35, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='1bq1' size='340' side='right'caption='[[1bq1]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1bq1' size='340' side='right'caption='[[1bq1]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bq1]] 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=1BQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BQ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bq1]] 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=1BQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BQ1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CB3:10~~-~~PROPARGYL-5~~,~~8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=UMP:~~2~~-DEOXYURIDINE+~~5~~-MONOPHOSPHATE'>UMP</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.5Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~CXM~~:N-~~CARBOXYMETHIONINE~~'>~~CXM~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class="sblockDat">THYA ([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/Thymidylate_synthase Thymidylate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45]~~ </~~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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [https://pdbe.org/1bq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [https://www.ebi.ac.uk/pdbsum/1bq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bq1 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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [https://pdbe.org/1bq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [https://www.ebi.ac.uk/pdbsum/1bq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bq1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TYSY_ECOLI TYSY_ECOLI]] Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation.	+	[https://www.uniprot.org/uniprot/TYSY_ECOLI TYSY_ECOLI] Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 22:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bq1 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=1bq1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Mutation of thymidylate synthase N229(177) to alanine results in an essentially inactive enzyme, yet it leads to formation of a stable ternary complex. The kinetics of N229(177)A show that kcat for Escherichia coli is reduced by 200-fold while the Km for dUMP is increased 200-fold and the Km for folate increased by tenfold versus the wild-type enzyme. The crystal structures of N229(177)A in complex with dUMP and CB3717, and in complex with dUMP alone are determined at 2.4 A, and 2.5 A resolution. These structures identify the covalently bound ternary complex and show how N229(177)A traps an intermediate, and so becomes inactive in a later step of the reaction. Since the smaller alanine side-chain at N229(177)A does not directly sterically impair binding of ligands, the structures implicate, and place quantitative limits on the involvement of the structured water network in the active site of thymidylate synthase in both catalysis and in determining the binding affinity for dUMP (in contrast, the N229(177)V mutation in Lactobacillus casei has minimal effect on activity).
-
-	Inactivity of N229A thymidylate synthase due to water-mediated effects: isolating a late stage in methyl transfer.,Reyes CL, Sage CR, Rutenber EE, Nissen RM, Finer-Moore JS, Stroud RM J Mol Biol. 1998 Dec 4;284(3):699-712. PMID:9826509<ref>PMID:9826509</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1bq1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Thymidylate synthase 3D structures\|Thymidylate synthase 3D structures]]		*[[Thymidylate synthase 3D structures\|Thymidylate synthase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Thymidylate synthase]]~~	+	[[Category: Finer-Moore JS]]
-	[[Category: Finer-Moore~~, J S~~]]	+	[[Category: Reyes CL]]
-	[[Category: Reyes~~, C L~~]]	+	[[Category: Rutenber EE]]
-	[[Category: Rutenber~~, E E~~]]	+	[[Category: Sage CR]]
-	[[Category: Sage~~, C R~~]]	+	[[Category: Stroud RM]]
-	[[Category: Stroud~~, R M]]~~	+
-	~~[[Category: Active site mutant]]~~	+
-	~~[[Category: Reaction intermediate]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 14:47, 3 November 2021

OCA — Wed, 03 Nov 2021 14:47:52 GMT

OCA at 10:15, 18 November 2020

OCA — Wed, 18 Nov 2020 10:15:09 GMT

←Older revision		Revision as of 10:15, 18 November 2020
Line 1:		Line 1:

	==E. COLI THYMIDYLATE SYNTHASE MUTANT N177A IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)==		==E. COLI THYMIDYLATE SYNTHASE MUTANT N177A IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)==
-	<StructureSection load='1bq1' size='340' side='right' caption='[[1bq1]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1bq1' size='340' side='right'caption='[[1bq1]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bq1]] 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=1BQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1BQ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bq1]] 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=1BQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1BQ1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">THYA ([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">THYA ([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/Thymidylate_synthase Thymidylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidylate_synthase Thymidylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [http://pdbe.org/1bq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1bq1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bq1 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [http://pdbe.org/1bq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1bq1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bq1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[Thymidylate synthase\|Thymidylate synthase]]	+	*[[Thymidylate synthase 3D structures\|Thymidylate synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Thymidylate synthase]]		[[Category: Thymidylate synthase]]
	[[Category: Finer-Moore, J S]]		[[Category: Finer-Moore, J S]]

OCA at 06:07, 4 April 2018

OCA — Wed, 04 Apr 2018 06:07:08 GMT

←Older revision		Revision as of 06:07, 4 April 2018
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bq/1bq1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bq/1bq1_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1bq1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1bq1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thymidylate synthase\|Thymidylate synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:20, 29 November 2017

OCA — Wed, 29 Nov 2017 08:20:46 GMT

←Older revision		Revision as of 08:20, 29 November 2017
Line 1:		Line 1:
		+
	==E. COLI THYMIDYLATE SYNTHASE MUTANT N177A IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)==		==E. COLI THYMIDYLATE SYNTHASE MUTANT N177A IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)==
	<StructureSection load='1bq1' size='340' side='right' caption='[[1bq1]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1bq1' size='340' side='right' caption='[[1bq1]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">THYA ([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">THYA ([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/Thymidylate_synthase Thymidylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidylate_synthase Thymidylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [http://pdbe.org/1bq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1bq1 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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [http://pdbe.org/1bq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1bq1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bq1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1bq1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1bq1" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Thymidylate synthase\|Thymidylate synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:33, 9 February 2016

OCA — Tue, 09 Feb 2016 04:33:43 GMT

←Older revision		Revision as of 04:33, 9 February 2016
Line 19:		Line 19:
	<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=1bq1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:40, 10 September 2015

OCA — Thu, 10 Sep 2015 18:40:28 GMT

←Older revision		Revision as of 18:40, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1bq1' size='340' side='right' caption='[[1bq1]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1bq1' size='340' side='right' caption='[[1bq1]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bq1]] 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=1BQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bq1]] 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=1BQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQ1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">THYA ([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">THYA ([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/Thymidylate_synthase Thymidylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidylate_synthase Thymidylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1bq1 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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [http://pdbe.org/1bq1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1bq1 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1bq1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Thymidylate synthase]]		[[Category: Thymidylate synthase]]
	[[Category: Finer-Moore, J S]]		[[Category: Finer-Moore, J S]]

OCA at 04:27, 25 December 2014

OCA — Thu, 25 Dec 2014 04:27:05 GMT

←Older revision		Revision as of 04:27, 25 December 2014
Line 9:		Line 9:
	<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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1bq1 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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1bq1 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TYSY_ECOLI TYSY_ECOLI]] Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 11:46, 22 December 2014

OCA — Mon, 22 Dec 2014 11:46:51 GMT

←Older revision		Revision as of 11:46, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bq1]] 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=1BQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQ1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bq1]] 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=1BQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQ1 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">THYA ([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">THYA ([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/Thymidylate_synthase Thymidylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thymidylate_synthase Thymidylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1bq1 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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1bq1 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Thymidylate synthase]]		[[Category: Thymidylate synthase]]
-	[[Category: Finer-Moore, J S.]]	+	[[Category: Finer-Moore, J S]]
-	[[Category: Reyes, C L.]]	+	[[Category: Reyes, C L]]
-	[[Category: Rutenber, E E.]]	+	[[Category: Rutenber, E E]]
-	[[Category: Sage, C R.]]	+	[[Category: Sage, C R]]
-	[[Category: Stroud, R M.]]	+	[[Category: Stroud, R M]]
	[[Category: Active site mutant]]		[[Category: Active site mutant]]
	[[Category: Reaction intermediate]]		[[Category: Reaction intermediate]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 09:49, 13 August 2014

OCA — Wed, 13 Aug 2014 09:49:04 GMT

←Older revision		Revision as of 09:49, 13 August 2014
Line 1:		Line 1:
-	[[~~Image:~~1bq1.~~png~~\|~~left~~\|200px]]	+	==E. COLI THYMIDYLATE SYNTHASE MUTANT N177A IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)==
		+	<StructureSection load='1bq1' size='340' side='right' caption='[[1bq1]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1bq1]] 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=1BQ1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BQ1 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">THYA ([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/Thymidylate_synthase Thymidylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [http://www.ebi.ac.uk/pdbsum/1bq1 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/bq/1bq1_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 ==
		+	Mutation of thymidylate synthase N229(177) to alanine results in an essentially inactive enzyme, yet it leads to formation of a stable ternary complex. The kinetics of N229(177)A show that kcat for Escherichia coli is reduced by 200-fold while the Km for dUMP is increased 200-fold and the Km for folate increased by tenfold versus the wild-type enzyme. The crystal structures of N229(177)A in complex with dUMP and CB3717, and in complex with dUMP alone are determined at 2.4 A, and 2.5 A resolution. These structures identify the covalently bound ternary complex and show how N229(177)A traps an intermediate, and so becomes inactive in a later step of the reaction. Since the smaller alanine side-chain at N229(177)A does not directly sterically impair binding of ligands, the structures implicate, and place quantitative limits on the involvement of the structured water network in the active site of thymidylate synthase in both catalysis and in determining the binding affinity for dUMP (in contrast, the N229(177)V mutation in Lactobacillus casei has minimal effect on activity).

-	~~{{STRUCTURE_1bq1\| PDB=1bq1 \| SCENE= }}~~	+	Inactivity of N229A thymidylate synthase due to water-mediated effects: isolating a late stage in methyl transfer.,Reyes CL, Sage CR, Rutenber EE, Nissen RM, Finer-Moore JS, Stroud RM J Mol Biol. 1998 Dec 4;284(3):699-712. PMID:9826509<ref>PMID:9826509</ref>

-	~~===E. COLI THYMIDYLATE SYNTHASE MUTANT N177A IN COMPLEX WITH CB3717 AND 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9826509}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1bq1]] 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=1BQ1 OCA].~~	+

	==See Also==		==See Also==
	*[[Thymidylate synthase\|Thymidylate synthase]]		*[[Thymidylate synthase\|Thymidylate synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:009826509<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Thymidylate synthase]]		[[Category: Thymidylate synthase]]

←Older revision		Revision as of 14:47, 3 November 2021
Line 3:		Line 3:
	<StructureSection load='1bq1' size='340' side='right'caption='[[1bq1]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1bq1' size='340' side='right'caption='[[1bq1]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bq1]] 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=1BQ1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1BQ1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bq1]] 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=1BQ1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BQ1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CB3:10-PROPARGYL-5,8-DIDEAZAFOLIC+ACID'>CB3</scene>, <scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CXM:N-CARBOXYMETHIONINE'>CXM</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">THYA ([~~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">THYA ([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/Thymidylate_synthase Thymidylate synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Thymidylate_synthase Thymidylate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.45 2.1.1.45] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [~~http~~://pdbe.org/1bq1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1bq1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1bq1 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=1bq1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bq1 OCA], [https://pdbe.org/1bq1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bq1 RCSB], [https://www.ebi.ac.uk/pdbsum/1bq1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bq1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TYSY_ECOLI TYSY_ECOLI]] Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation.	+	[[https://www.uniprot.org/uniprot/TYSY_ECOLI TYSY_ECOLI]] Provides the sole de novo source of dTMP for DNA biosynthesis. This protein also binds to its mRNA thus repressing its own translation.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]