1e0d - Revision history

OCA at 08:09, 6 December 2023

OCA — Wed, 06 Dec 2023 08:09:48 GMT

←Older revision		Revision as of 08:09, 6 December 2023
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	<StructureSection load='1e0d' size='340' side='right'caption='[[1e0d]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1e0d' size='340' side='right'caption='[[1e0d]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1e0d]] is a 1 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=1E0D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1E0D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1e0d]] is a 1 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=1E0D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E0D FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>MURD GENE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </~~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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [https://pdbe.org/1e0d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [https://www.ebi.ac.uk/pdbsum/1e0d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e0d 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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [~~http~~://pdbe.org/1e0d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1e0d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1e0d ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MURD_ECOLI MURD_ECOLI]] Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA).[HAMAP-Rule:MF_00639]	+	[https://www.uniprot.org/uniprot/MURD_ECOLI MURD_ECOLI] Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA).[HAMAP-Rule:MF_00639]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]~~	+	[[Category: Bertrand J]]
-	[[Category: Bertrand, J]]	+	[[Category: Chantalat L]]
-	[[Category: Chantalat, L]]	+	[[Category: Dideberg O]]
-	[[Category: Dideberg, O]]	+	[[Category: Fanchon E]]
-	[[Category: Fanchon, E]]	+
-	~~[[Category: Adp-forming enzyme]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Murd]]~~	+
-	~~[[Category: Peptidoglycan synthesis~~]]	+

OCA at 10:22, 18 November 2020

OCA — Wed, 18 Nov 2020 10:22:02 GMT

←Older revision		Revision as of 10:22, 18 November 2020
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	==UDP-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase==		==UDP-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase==
-	<StructureSection load='1e0d' size='340' side='right' caption='[[1e0d]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1e0d' size='340' side='right'caption='[[1e0d]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1e0d]] is a 1 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=1E0D OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1E0D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1e0d]] is a 1 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=1E0D OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1E0D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MURD GENE ([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">MURD GENE ([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/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [http://pdbe.org/1e0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [http://www.ebi.ac.uk/pdbsum/1e0d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1e0d 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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [http://pdbe.org/1e0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [http://www.ebi.ac.uk/pdbsum/1e0d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1e0d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]		[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]
	[[Category: Bertrand, J]]		[[Category: Bertrand, J]]

OCA at 07:47, 14 June 2018

OCA — Thu, 14 Jun 2018 07:47:02 GMT

←Older revision		Revision as of 07:47, 14 June 2018
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-	==UDP-N-~~ACETYLMURAMOYL~~-L-~~ALANINE~~:D-~~GLUTAMATE LIGASE~~==	+	==UDP-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase==
	<StructureSection load='1e0d' size='340' side='right' caption='[[1e0d]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1e0d' size='340' side='right' caption='[[1e0d]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1e0d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1e0d" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Mur ligase\|Mur ligase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:58, 13 December 2017

OCA — Wed, 13 Dec 2017 07:58:33 GMT

←Older revision		Revision as of 07:58, 13 December 2017
Line 1:		Line 1:
		+
	==UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE==		==UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE==
	<StructureSection load='1e0d' size='340' side='right' caption='[[1e0d]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1e0d' size='340' side='right' caption='[[1e0d]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MURD GENE ([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">MURD GENE ([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/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [http://pdbe.org/1e0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [http://www.ebi.ac.uk/pdbsum/1e0d 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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [http://pdbe.org/1e0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [http://www.ebi.ac.uk/pdbsum/1e0d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1e0d 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/e0/1e0d_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e0/1e0d_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 1e0d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1e0d" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[MurD ligase\|MurD ligase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:31, 7 February 2016

OCA — Sun, 07 Feb 2016 20:31:28 GMT

←Older revision		Revision as of 20:31, 7 February 2016
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	<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=1e0d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:36, 27 January 2016

OCA — Wed, 27 Jan 2016 18:36:05 GMT

←Older revision		Revision as of 18:36, 27 January 2016
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1e0d]] is a 1 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=1E0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E0D FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e0d]] is a 1 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=1E0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E0D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MURD GENE ([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">MURD GENE ([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/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </span></td></tr>
Line 23:		Line 22:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ~~ligase~~ (MurD) ~~is a cytoplasmic enzyme involved in the biosynthesis of peptidoglycan which catalyzes~~ the addition of D-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). The crystal ~~structure~~ of ~~MurD~~ in the ~~presence of its~~ substrate UMA ~~has~~ been ~~solved to~~ 1.9 A resolution~~. Phase information was obtained from multiple anomalous dispersion using the K-shell edge of selenium in combination with multiple isomorphous replacement~~. The structure comprises three domains of topology ~~each~~ reminiscent of nucleotide-binding folds: the ~~N- and~~ C-terminal ~~domains are consistent with the dinucleotide~~-~~binding fold called~~ the ~~Rossmann fold,~~ and ~~the~~ central ~~domain~~ with the ~~mononucleotide-binding fold also observed in the GTPase family~~. ~~The structure~~ reveals the binding ~~site~~ of ~~the substrate~~ UMA, and ~~comparison with known NTP complexes~~ allows the identification of residues ~~interacting with ATP~~. The ~~study describes~~ the ~~first structure~~ of the ~~UDP-N-acetylmuramoyl-peptide~~ ligase ~~family~~.	+	UDP-N-acetylmuramoyl-l-alanine:d-glutamate (MurD) ligase catalyses the addition of d-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-l-alanine (UMA). The crystal structures of Escherichia coli in the substrate-free form and MurD complexed with UMA have been determined at 2.4 A and 1.88 A resolution, respectively. The MurD structure comprises three domains each of a topology reminiscent of nucleotide-binding folds. In the two structures the C-terminal domain undergoes a large rigid-body rotation away from the N-terminal and central domains. These two "open" structures were compared with the four published "closed" structures of MurD. In addition the comparison reveals which regions are affected by the binding of UMA, ATP and d-Glu. Also we compare and discuss two structurally characterized enzymes which belong to the same ligase superfamily: MurD and folylpolyglutamate synthetase (FGS). The analysis allows the identification of key residues involved in the reaction mechanism of FGS. The determination of the two "open" conformation structures represents a new step towards the complete elucidation of the enzymatic mechanism of the MurD ligase.

-	~~Crystal structure~~ of ~~UDP-N-acetylmuramoyl-L-alanine~~:~~D-glutamate ligase from Escherichia coli~~.,Bertrand JA~~, Auger G~~, Fanchon E, Martin L, Blanot D, van Heijenoort J, Dideberg O ~~EMBO~~ J. ~~1997 Jun 16~~;16(12):~~3416~~-25. PMID:~~9218784~~<ref>PMID:~~9218784~~</ref>	+	"Open" structures of MurD: domain movements and structural similarities with folylpolyglutamate synthetase.,Bertrand JA, Fanchon E, Martin L, Chantalat L, Auger G, Blanot D, van Heijenoort J, Dideberg O J Mol Biol. 2000 Sep 1;301(5):1257-66. PMID:10966819<ref>PMID:10966819</ref>

	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>

OCA at 04:45, 10 September 2015

OCA — Thu, 10 Sep 2015 04:45:01 GMT

←Older revision		Revision as of 04:45, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1e0d' size='340' side='right' caption='[[1e0d]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1e0d' size='340' side='right' caption='[[1e0d]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1e0d]] is a 1 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=1E0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E0D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1e0d]] is a 1 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=1E0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E0D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MURD GENE ([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">MURD GENE ([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/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [http://www.ebi.ac.uk/pdbsum/1e0d 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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [http://pdbe.org/1e0d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [http://www.ebi.ac.uk/pdbsum/1e0d 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 1e0d" 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: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]		[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]
	[[Category: Bertrand, J]]		[[Category: Bertrand, J]]

OCA at 18:04, 24 December 2014

OCA — Wed, 24 Dec 2014 18:04:37 GMT

←Older revision		Revision as of 18:04, 24 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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [http://www.ebi.ac.uk/pdbsum/1e0d 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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [http://www.ebi.ac.uk/pdbsum/1e0d PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MURD_ECOLI MURD_ECOLI]] Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA).[HAMAP-Rule:MF_00639]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 19:23, 22 December 2014

OCA — Mon, 22 Dec 2014 19:23:53 GMT

←Older revision		Revision as of 19:23, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1e0d]] is a 1 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=1E0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E0D FirstGlance]. <br>		<table><tr><td colspan='2'>[[1e0d]] is a 1 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=1E0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E0D FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MURD GENE ([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">MURD GENE ([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/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [http://www.ebi.ac.uk/pdbsum/1e0d 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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [http://www.ebi.ac.uk/pdbsum/1e0d 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: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]		[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]
-	[[Category: Bertrand, J.]]	+	[[Category: Bertrand, J]]
-	[[Category: Chantalat, L.]]	+	[[Category: Chantalat, L]]
-	[[Category: Dideberg, O.]]	+	[[Category: Dideberg, O]]
-	[[Category: Fanchon, E.]]	+	[[Category: Fanchon, E]]
	[[Category: Adp-forming enzyme]]		[[Category: Adp-forming enzyme]]
	[[Category: Ligase]]		[[Category: Ligase]]
	[[Category: Murd]]		[[Category: Murd]]
	[[Category: Peptidoglycan synthesis]]		[[Category: Peptidoglycan synthesis]]

OCA at 04:10, 3 October 2014

OCA — Fri, 03 Oct 2014 04:10:48 GMT

←Older revision		Revision as of 04:10, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1e0d~~\| ~~PDB~~=1e0d \| ~~SCENE~~= }}	+	==UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE==
-	===UDP-N-~~ACETYLMURAMOYL~~-L-~~ALANINE:~~D-~~GLUTAMATE LIGASE~~===	+	<StructureSection load='1e0d' size='340' side='right' caption='[[1e0d]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_9218784}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1e0d]] is a 1 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=1E0D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1E0D FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1uag\|1uag]], [[2uag\|2uag]], [[3uag\|3uag]], [[4uag\|4uag]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MURD GENE ([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/UDP-N-acetylmuramoyl-L-alanine--D-glutamate_ligase UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.9 6.3.2.9] </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=1e0d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e0d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1e0d RCSB], [http://www.ebi.ac.uk/pdbsum/1e0d 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/e0/1e0d_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 ==
		+	UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD) is a cytoplasmic enzyme involved in the biosynthesis of peptidoglycan which catalyzes the addition of D-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA). The crystal structure of MurD in the presence of its substrate UMA has been solved to 1.9 A resolution. Phase information was obtained from multiple anomalous dispersion using the K-shell edge of selenium in combination with multiple isomorphous replacement. The structure comprises three domains of topology each reminiscent of nucleotide-binding folds: the N- and C-terminal domains are consistent with the dinucleotide-binding fold called the Rossmann fold, and the central domain with the mononucleotide-binding fold also observed in the GTPase family. The structure reveals the binding site of the substrate UMA, and comparison with known NTP complexes allows the identification of residues interacting with ATP. The study describes the first structure of the UDP-N-acetylmuramoyl-peptide ligase family.

-	~~==About this Structure==~~	+	Crystal structure of UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase from Escherichia coli.,Bertrand JA, Auger G, Fanchon E, Martin L, Blanot D, van Heijenoort J, Dideberg O EMBO J. 1997 Jun 16;16(12):3416-25. PMID:9218784<ref>PMID:9218784</ref>
-	~~[[1e0d]] is a 1 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=1E0D OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:009218784</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[MurD ligase\|MurD ligase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]		[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]