1njd - Revision history

OCA at 07:57, 14 February 2024

OCA — Wed, 14 Feb 2024 07:57:19 GMT

←Older revision		Revision as of 07:57, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1njd' size='340' side='right'caption='[[1njd]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1njd' size='340' side='right'caption='[[1njd]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1njd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_a"_von_freudenreich_1890 "bacillus a" von freudenreich 1890~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1njd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lacticaseibacillus_casei Lacticaseibacillus casei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJD FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<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]] 2.2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>N229D MUTANT OF CLONED L. CASE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1582~~ "~~Bacillus a~~" ~~von Freudenreich 1890])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [https://pdbe.org/1njd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [https://www.ebi.ac.uk/pdbsum/1njd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1njd 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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [https://pdbe.org/1njd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [https://www.ebi.ac.uk/pdbsum/1njd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1njd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TYSY_LACCA TYSY_LACCA]] Provides the sole de novo source of dTMP for DNA biosynthesis.	+	[https://www.uniprot.org/uniprot/TYSY_LACCA TYSY_LACCA] Provides the sole de novo source of dTMP for DNA biosynthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		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=1njd 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=1njd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Thymidylate synthase (TS) methylates only dUMP, not dCMP. The crystal structure of TS.dCMP shows sCMP 4-NH2 excluded from the space between Asn-229 and His-199 by the hydrogen bonding and steric properties and Asn-229. Consequently, 6-C of dCMP is over 4 A from the active site sulfhydryl. The Asn-229 side chain is prevented from flipping 180 degrees to and orientation the could hydrogen bond to dCMP by a hydrogen bond network between conserved residues. Thus, the specific binding of dUMP by TS results from occlusion of competing substrates by steric and electronic effects of residues in the active site cavity. When Asn-229 is replaced by a cysteine, the Cys-229 S gamma rotates out of the active site, and the mutant enzyme binds both dCMP and dUMP tightly but does not methylate dCMP. Thus simply admitting dCMP into the dUMP binding site of TS is not sufficient for methylation of dCMP. Structures of nucleotide complexes of TS N229D provide a reasonable explanation for the preferential methylation of dCMP instead of dUMP by this mutant. In TS N229D.dCMP, Asp-229 forms hydrogen bonds to 3-N and 40NH2 of dCMP. Neither the Asp-229 carboxyl moiety nor ordered water appears to hydrogen bond to 4-O of dUMP. Hydrogen bonds to 4-O (or 4-NH2) have been proposed to stabilize reaction intermediates. If their absence in TS N229D.dUMP persists in the ternary complex, it could explain the 10(4)-fold decrease in kcat/Km for dUMP.
-
-	Partitioning roles of side chains in affinity, orientation, and catalysis with structures for mutant complexes: asparagine-229 in thymidylate synthase.,Finer-Moore JS, Liu L, Schafmeister CE, Birdsall DL, Mau T, Santi DV, Stroud RM Biochemistry. 1996 Apr 23;35(16):5125-36. PMID:8611496<ref>PMID:8611496</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1njd" 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 a von freudenreich 1890~~]]	+	[[Category: Lacticaseibacillus casei]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Thymidylate synthase]]~~	+	[[Category: Finer-Moore J]]
-	[[Category: Finer-Moore, J]]	+	[[Category: Stroud RM]]
-	[[Category: Stroud~~, R M]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Nucleotide biosynthesis]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 15:23, 3 November 2021

OCA — Wed, 03 Nov 2021 15:23:55 GMT

←Older revision		Revision as of 15:23, 3 November 2021
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	<StructureSection load='1njd' size='340' side='right'caption='[[1njd]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1njd' size='340' side='right'caption='[[1njd]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1njd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_a"_von_freudenreich_1890 "bacillus a" von freudenreich 1890]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1NJD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1njd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_a"_von_freudenreich_1890 "bacillus a" von freudenreich 1890]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NJD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N229D MUTANT OF CLONED L. CASE ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1582 "Bacillus a" von Freudenreich 1890])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N229D MUTANT OF CLONED L. CASE ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1582 "Bacillus a" von Freudenreich 1890])</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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [~~http~~://pdbe.org/1njd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1njd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1njd 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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [https://pdbe.org/1njd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [https://www.ebi.ac.uk/pdbsum/1njd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1njd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TYSY_LACCA TYSY_LACCA]] Provides the sole de novo source of dTMP for DNA biosynthesis.	+	[[https://www.uniprot.org/uniprot/TYSY_LACCA TYSY_LACCA]] Provides the sole de novo source of dTMP for DNA biosynthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:51, 2 December 2020

OCA — Wed, 02 Dec 2020 08:51:37 GMT

←Older revision		Revision as of 08:51, 2 December 2020
Line 1:		Line 1:

	==THYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)==		==THYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)==
-	<StructureSection load='1njd' size='340' side='right' caption='[[1njd]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1njd' size='340' side='right'caption='[[1njd]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1njd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_a"_von_freudenreich_1890 "bacillus a" von freudenreich 1890]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1NJD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1njd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_a"_von_freudenreich_1890 "bacillus a" von freudenreich 1890]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NJD FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N229D MUTANT OF CLONED L. CASE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1582 "Bacillus a" von Freudenreich 1890])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N229D MUTANT OF CLONED L. CASE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1582 "Bacillus a" von Freudenreich 1890])</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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [http://pdbe.org/1njd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [http://www.ebi.ac.uk/pdbsum/1njd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1njd 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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [http://pdbe.org/1njd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [http://www.ebi.ac.uk/pdbsum/1njd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1njd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1njd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1njd" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Thymidylate synthase 3D structures\|Thymidylate synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 35:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus a von freudenreich 1890]]		[[Category: Bacillus a von freudenreich 1890]]
		+	[[Category: Large Structures]]
	[[Category: Thymidylate synthase]]		[[Category: Thymidylate synthase]]
	[[Category: Finer-Moore, J]]		[[Category: Finer-Moore, J]]

OCA at 07:34, 7 February 2018

OCA — Wed, 07 Feb 2018 07:34:22 GMT

←Older revision		Revision as of 07:34, 7 February 2018
Line 1:		Line 1:
		+
	==THYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)==		==THYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)==
	<StructureSection load='1njd' size='340' side='right' caption='[[1njd]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1njd' size='340' side='right' caption='[[1njd]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N229D MUTANT OF CLONED L. CASE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1582 "Bacillus a" von Freudenreich 1890])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N229D MUTANT OF CLONED L. CASE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1582 "Bacillus a" von Freudenreich 1890])</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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [http://pdbe.org/1njd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [http://www.ebi.ac.uk/pdbsum/1njd 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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [http://pdbe.org/1njd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [http://www.ebi.ac.uk/pdbsum/1njd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1njd ProSAT]</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/nj/1njd_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nj/1njd_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1njd" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1njd" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Thymidylate synthase\|Thymidylate synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:35, 9 February 2016

OCA — Tue, 09 Feb 2016 08:35:24 GMT

←Older revision		Revision as of 08:35, 9 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=1njd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:30, 10 September 2015

OCA — Thu, 10 Sep 2015 20:30:29 GMT

←Older revision		Revision as of 20:30, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1njd' size='340' side='right' caption='[[1njd]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1njd' size='340' side='right' caption='[[1njd]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1njd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Lactobacillus_casei Lactobacillus casei~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJD FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1njd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_a"_von_freudenreich_1890 "bacillus a" von freudenreich 1890]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N229D MUTANT OF CLONED L. CASE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1582 ~~Lactobacillus casei~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N229D MUTANT OF CLONED L. CASE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1582 "Bacillus a" von Freudenreich 1890])</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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [http://www.ebi.ac.uk/pdbsum/1njd 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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [http://pdbe.org/1njd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [http://www.ebi.ac.uk/pdbsum/1njd PDBsum]</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 1njd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lactobacillus casei~~]]	+	[[Category: Bacillus a von freudenreich 1890]]
	[[Category: Thymidylate synthase]]		[[Category: Thymidylate synthase]]
	[[Category: Finer-Moore, J]]		[[Category: Finer-Moore, J]]

OCA at 05:45, 25 December 2014

OCA — Thu, 25 Dec 2014 05:45:41 GMT

←Older revision		Revision as of 05:45, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1njd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_casei Lactobacillus casei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJD FirstGlance]. <br>		<table><tr><td colspan='2'>[[1njd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_casei Lactobacillus casei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJD FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N229D MUTANT OF CLONED L. CASE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1582 Lactobacillus casei])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N229D MUTANT OF CLONED L. CASE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1582 Lactobacillus casei])</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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [http://www.ebi.ac.uk/pdbsum/1njd 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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [http://www.ebi.ac.uk/pdbsum/1njd PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TYSY_LACCA TYSY_LACCA]] Provides the sole de novo source of dTMP for DNA biosynthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: Lactobacillus casei]]		[[Category: Lactobacillus casei]]
	[[Category: Thymidylate synthase]]		[[Category: Thymidylate synthase]]
-	[[Category: Finer-Moore, J.]]	+	[[Category: Finer-Moore, J]]
-	[[Category: Stroud, R M.]]	+	[[Category: Stroud, R M]]
	[[Category: Methyltransferase]]		[[Category: Methyltransferase]]
	[[Category: Nucleotide biosynthesis]]		[[Category: Nucleotide biosynthesis]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 16:17, 28 September 2014

OCA — Sun, 28 Sep 2014 16:17:22 GMT

←Older revision		Revision as of 16:17, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1njd.~~png~~\|~~left~~\|200px]]	+	==THYMIDYLATE SYNTHASE, MUTATION, N229D WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)==
		+	<StructureSection load='1njd' size='340' side='right' caption='[[1njd]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1njd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_casei Lactobacillus casei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NJD FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UMP:2-DEOXYURIDINE+5-MONOPHOSPHATE'>UMP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">N229D MUTANT OF CLONED L. CASE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1582 Lactobacillus casei])</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=1njd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1njd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1njd RCSB], [http://www.ebi.ac.uk/pdbsum/1njd 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/nj/1njd_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 ==
		+	Thymidylate synthase (TS) methylates only dUMP, not dCMP. The crystal structure of TS.dCMP shows sCMP 4-NH2 excluded from the space between Asn-229 and His-199 by the hydrogen bonding and steric properties and Asn-229. Consequently, 6-C of dCMP is over 4 A from the active site sulfhydryl. The Asn-229 side chain is prevented from flipping 180 degrees to and orientation the could hydrogen bond to dCMP by a hydrogen bond network between conserved residues. Thus, the specific binding of dUMP by TS results from occlusion of competing substrates by steric and electronic effects of residues in the active site cavity. When Asn-229 is replaced by a cysteine, the Cys-229 S gamma rotates out of the active site, and the mutant enzyme binds both dCMP and dUMP tightly but does not methylate dCMP. Thus simply admitting dCMP into the dUMP binding site of TS is not sufficient for methylation of dCMP. Structures of nucleotide complexes of TS N229D provide a reasonable explanation for the preferential methylation of dCMP instead of dUMP by this mutant. In TS N229D.dCMP, Asp-229 forms hydrogen bonds to 3-N and 40NH2 of dCMP. Neither the Asp-229 carboxyl moiety nor ordered water appears to hydrogen bond to 4-O of dUMP. Hydrogen bonds to 4-O (or 4-NH2) have been proposed to stabilize reaction intermediates. If their absence in TS N229D.dUMP persists in the ternary complex, it could explain the 10(4)-fold decrease in kcat/Km for dUMP.

-	~~{{STRUCTURE_1njd\| PDB=1njd \| SCENE= }}~~	+	Partitioning roles of side chains in affinity, orientation, and catalysis with structures for mutant complexes: asparagine-229 in thymidylate synthase.,Finer-Moore JS, Liu L, Schafmeister CE, Birdsall DL, Mau T, Santi DV, Stroud RM Biochemistry. 1996 Apr 23;35(16):5125-36. PMID:8611496<ref>PMID:8611496</ref>

-	~~===THYMIDYLATE SYNTHASE~~, ~~MUTATION, N229D WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_8611496}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1njd]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Lactobacillus_casei Lactobacillus casei]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA].~~	+

	==See Also==		==See Also==
	*[[Thymidylate synthase\|Thymidylate synthase]]		*[[Thymidylate synthase\|Thymidylate synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:008611496<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Lactobacillus casei]]		[[Category: Lactobacillus casei]]
	[[Category: Thymidylate synthase]]		[[Category: Thymidylate synthase]]

OCA at 13:17, 20 October 2012

OCA — Sat, 20 Oct 2012 13:17:38 GMT

←Older revision		Revision as of 13:17, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1njd]] is a 1 chain structure ~~of [[Thymidylate synthase]]~~ with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_casei Lactobacillus casei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA].	+	[[1njd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lactobacillus_casei Lactobacillus casei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NJD OCA].

	==See Also==		==See Also==

OCA: Protected "1njd" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 11:30:16 GMT

Protected "1njd" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:30, 26 July 2012