4uag: Difference between revisions

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-{{Seed}}
-[[Image:4uag.png|left|200px]]
-<!--
+==UDP-N-ACETYLMURAMOYL-L-ALANINE:D-GLUTAMATE LIGASE==
-The line below this paragraph, containing "STRUCTURE_4uag", creates the "Structure Box" on the page.
+<StructureSection load='4uag' size='340' side='right'caption='[[4uag]], [[Resolution|resolution]] 1.66&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[4uag]] 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=4UAG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UAG FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.66&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UAG:URIDINE-5-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE'>UAG</scene>, <scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-{{STRUCTURE_4uag|  PDB=4uag  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4uag FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uag OCA], [https://pdbe.org/4uag PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uag RCSB], [https://www.ebi.ac.uk/pdbsum/4uag PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uag 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/4uag_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=4uag 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 4uag" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_10356330}}, adds the Publication Abstract to the page
+*[[Mur ligase|Mur ligase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 10356330 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_10356330}}
+__TOC__
+</StructureSection>
-==About this Structure==
-UAG is a 1 chain 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=4UAG OCA].
-==Reference==
-<ref group="xtra">PMID:10356330</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]
+[[Category: Large Structures]]
-[[Category: Auger, G.]]
+[[Category: Auger G]]
-[[Category: Beller, D Le.]]
+[[Category: Bertrand J]]
-[[Category: Bertrand, J.]]
+[[Category: Blanot D]]
-[[Category: Blanot, D.]]
+[[Category: Dideberg O]]
-[[Category: Dideberg, O.]]
+[[Category: Fanchon E]]
-[[Category: Fanchon, E.]]
+[[Category: Le Beller D]]
-[[Category: Heijenoort, J Van.]]
+[[Category: Martin L]]
-[[Category: Martin, L.]]
+[[Category: Van Heijenoort J]]
-[[Category: Adp-forming enzyme]]
-[[Category: Ligase]]
-[[Category: Murd]]
-[[Category: Peptidoglycan synthesis]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:17:22 2009''