2jff: Difference between revisions

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-{{Seed}}
-[[Image:2jff.png|left|200px]]
-<!--
+==Crystal structure of MurD ligase in complex with D-Glu containing sulfonamide inhibitor==
-The line below this paragraph, containing "STRUCTURE_2jff", creates the "Structure Box" on the page.
+<StructureSection load='2jff' size='340' side='right'caption='[[2jff]], [[Resolution|resolution]] 1.89&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'>[[2jff]] 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=2JFF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JFF 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]] 1.89&#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=LK2:N-[(6-BUTOXYNAPHTHALEN-2-YL)SULFONYL]-D-GLUTAMIC+ACID'>LK2</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_2jff|  PDB=2jff  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jff OCA], [https://pdbe.org/2jff PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jff RCSB], [https://www.ebi.ac.uk/pdbsum/2jff PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jff 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/jf/2jff_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=2jff ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Mur ligases play an essential role in the intracellular biosynthesis of bacterial peptidoglycan, the main component of the bacterial cell wall, and represent attractive targets for the design of novel antibacterials. UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase (MurD) catalyses the addition of D-glutamic acid to the cytoplasmic intermediate UDP-N-acetylmuramoyl-L-alanine (UMA) and is the second in the series of Mur ligases. MurD ligase is highly stereospecific for its substrate, D-glutamic acid (D-Glu). Here, we report the high resolution crystal structures of MurD in complexes with two novel inhibitors designed to mimic the transition state of the reaction, which contain either the D-Glu or the L-Glu moiety. The binding modes of N-sulfonyl-D-Glu and N-sulfonyl-L-Glu derivatives were also characterised kinetically. The results of this study represent an excellent starting point for further development of novel inhibitors of this enzyme.
-===CRYSTAL STRUCTURE OF MURD LIGASE IN COMPLEX WITH D-GLU CONTAINING SULFONAMIDE INHIBITOR===
+Structural and functional characterization of enantiomeric glutamic acid derivatives as potential transition state analogue inhibitors of MurD ligase.,Kotnik M, Humljan J, Contreras-Martel C, Oblak M, Kristan K, Herve M, Blanot D, Urleb U, Gobec S, Dessen A, Solmajer T J Mol Biol. 2007 Jun 29;370(1):107-15. Epub 2007 May 4. PMID:17507028<ref>PMID:17507028</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2jff" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17507028}}, adds the Publication Abstract to the page
+*[[Mur ligase|Mur ligase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17507028 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17507028}}
+__TOC__
+</StructureSection>
-==About this Structure==
-JFF 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=2JFF OCA].
-==Reference==
-<ref group="xtra">PMID:17507028</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: UDP-N-acetylmuramoyl-L-alanine--D-glutamate ligase]]
+[[Category: Large Structures]]
-[[Category: Blanot, D.]]
+[[Category: Blanot D]]
-[[Category: Contreras-Martel, C.]]
+[[Category: Contreras-Martel C]]
-[[Category: Dessen, A.]]
+[[Category: Dessen A]]
-[[Category: Gobec, S.]]
+[[Category: Gobec S]]
-[[Category: Herve, M.]]
+[[Category: Herve M]]
-[[Category: Humljan, J.]]
+[[Category: Humljan J]]
-[[Category: Kotnik, M.]]
+[[Category: Kotnik M]]
-[[Category: Kristan, K.]]
+[[Category: Kristan K]]
-[[Category: Oblak, M.]]
+[[Category: Oblak M]]
-[[Category: Solmajer, T.]]
+[[Category: Solmajer T]]
-[[Category: Urleb, U.]]
+[[Category: Urleb U]]
-[[Category: Atp-binding]]
-[[Category: Cell cycle]]
-[[Category: Cell division]]
-[[Category: Cell shape]]
-[[Category: Cell wall]]
-[[Category: Ligase]]
-[[Category: Murd ligase]]
-[[Category: Murd-inhibitor complex]]
-[[Category: Nucleotide-binding]]
-[[Category: Peptidoglycan synthesis]]
-[[Category: Sulfonamide inhibitor]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:19:02 2009''