3uag: Difference between revisions

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-[[Image:3uag.jpg|left|200px]]
- {{Structure
+==UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE==
-|PDB= 3uag |SIZE=350|CAPTION= <scene name='initialview01'>3uag</scene>, resolution 1.77&Aring;
+<StructureSection load='3uag' size='340' side='right'caption='[[3uag]], [[Resolution|resolution]] 1.77&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UMA:URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</scene>, <scene name='pdbligand=ADP:ADENOSINE-5'-DIPHOSPHATE'>ADP</scene> and <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID'>EPE</scene>
+<table><tr><td colspan='2'>[[3uag]] 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=3UAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UAG FirstGlance]. <br>
-|ACTIVITY= [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]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.77&#8491;</td></tr>
-|GENE= MURD GENE ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=UMA:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE'>UMA</scene></td></tr>
-}}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3uag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3uag OCA], [https://pdbe.org/3uag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3uag RCSB], [https://www.ebi.ac.uk/pdbsum/3uag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3uag ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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 ==
+[[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/ua/3uag_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/main_output.php?pdb_ID=3uag ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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 three complexes of Escherichia coli MurD with a variety of substrates and products have been determined to high resolution. These include (1) the quaternary complex of MurD, the substrate UMA, the product ADP, and Mg2+, (2) the quaternary complex of MurD, the substrate UMA, the product ADP, and Mn2+, and (3) the binary complex of MurD with the product UDP - N- acetylmuramoyl- L -alanine- D -glutamate (UMAG). The reaction mechanism supported by these structures proceeds by the phosphorylation of the C-terminal carboxylate group of UMA by the gamma-phosphate group of ATP to form an acyl-phosphate intermediate, followed by the nucleophilic attack by the amino group of D-glutamate to produce UMAG. A key feature in the reaction intermediate is the presence of two magnesium ions bridging negatively charged groups.
-'''UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE'''
+Determination of the MurD mechanism through crystallographic analysis of enzyme complexes.,Bertrand JA, Auger G, Martin L, Fanchon E, Blanot D, Le Beller D, van Heijenoort J, Dideberg O J Mol Biol. 1999 Jun 11;289(3):579-90. PMID:10356330<ref>PMID:10356330</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3uag" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-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 three complexes of Escherichia coli MurD with a variety of substrates and products have been determined to high resolution. These include (1) the quaternary complex of MurD, the substrate UMA, the product ADP, and Mg2+, (2) the quaternary complex of MurD, the substrate UMA, the product ADP, and Mn2+, and (3) the binary complex of MurD with the product UDP - N- acetylmuramoyl- L -alanine- D -glutamate (UMAG). The reaction mechanism supported by these structures proceeds by the phosphorylation of the C-terminal carboxylate group of UMA by the gamma-phosphate group of ATP to form an acyl-phosphate intermediate, followed by the nucleophilic attack by the amino group of D-glutamate to produce UMAG. A key feature in the reaction intermediate is the presence of two magnesium ions bridging negatively charged groups.
+*[[Mur ligase|Mur ligase]]
+== References ==
-==About this Structure==
+<references/>
-UAG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UAG OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Determination of the MurD mechanism through crystallographic analysis of enzyme complexes., Bertrand JA, Auger G, Martin L, Fanchon E, Blanot D, Le Beller D, van Heijenoort J, Dideberg O, J Mol Biol. 1999 Jun 11;289(3):579-90. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10356330 10356330]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]
+[[Category: Auger G]]
-[[Category: Auger, G.]]
+[[Category: Bertrand JA]]
-[[Category: Beller, D Le.]]
+[[Category: Blanot D]]
-[[Category: Bertrand, J A.]]
+[[Category: Dideberg O]]
-[[Category: Blanot, D.]]
+[[Category: Fanchon E]]
-[[Category: Dideberg, O.]]
+[[Category: Le Beller D]]
-[[Category: Fanchon, E.]]
+[[Category: Martin L]]
-[[Category: Heijenoort, J Van.]]
+[[Category: Van Heijenoort J]]
-[[Category: Martin, L.]]
-[[Category: ADP]]
-[[Category: EPE]]
-[[Category: MN]]
-[[Category: UMA]]
-[[Category: adp-forming enzyme]]
-[[Category: ligase]]
-[[Category: murd]]
-[[Category: peptidoglycan synthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 19:07:38 2008''