2fem: Difference between revisions

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 ==Mutant R188M of the Cytidine Monophosphate Kinase From E. Coli==
-<StructureSection load='2fem' size='340' side='right' caption='[[2fem]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='2fem' size='340' side='right'caption='[[2fem]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2fem]] 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=2FEM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FEM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2fem]] 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=2FEM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FEM FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2feo|2feo]]</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]] 1.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cmk, mssA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</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=2fem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fem OCA], [https://pdbe.org/2fem PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fem RCSB], [https://www.ebi.ac.uk/pdbsum/2fem PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fem ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytidylate_kinase Cytidylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </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=2fem FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fem OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fem RCSB], [http://www.ebi.ac.uk/pdbsum/2fem PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KCY_ECOLI KCY_ECOLI]] ATP, dATP, and GTP are equally effective as phosphate donors. CMP and dCMP are the best phosphate acceptors.<ref>PMID:8190075</ref> <ref>PMID:7836281</ref>
+[https://www.uniprot.org/uniprot/KCY_ECOLI KCY_ECOLI] ATP, dATP, and GTP are equally effective as phosphate donors. CMP and dCMP are the best phosphate acceptors.<ref>PMID:8190075</ref> <ref>PMID:7836281</ref>
 == 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/fe/2fem_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fe/2fem_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].
+</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=2fem ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Bacterial CMP kinases are specific for CMP and dCMP, whereas the related eukaryotic NMP kinase phosphorylates CMP and UMP with similar efficiency. To explain these differences in structural terms, we investigated the contribution of four key amino acids interacting with the pyrimidine ring of CMP (Ser36, Asp132, Arg110 and Arg188) to the stability, catalysis and substrate specificity of Escherichia coli CMP kinase. In contrast to eukaryotic UMP/CMP kinases, which interact with the nucleobase via one or two water molecules, bacterial CMP kinase has a narrower NMP-binding pocket and a hydrogen-bonding network involving the pyrimidine moiety specific for the cytosine nucleobase. The side chains of Arg110 and Ser36 cannot establish hydrogen bonds with UMP, and their substitution by hydrophobic amino acids simultaneously affects the K(m) of CMP/dCMP and the k(cat) value. Substitution of Ser for Asp132 results in a moderate decrease in stability without significant changes in K(m) value for CMP and dCMP. Replacement of Arg188 with Met does not affect enzyme stability but dramatically decreases the k(cat)/K(m) ratio compared with wild-type enzyme. This effect might be explained by opening of the enzyme/nucleotide complex, so that the sugar no longer interacts with Asp185. The reaction rate for different modified CMP kinases with ATP as a variable substrate indicated that none of changes induced by these amino acid substitutions was 'propagated' to the ATP subsite. This 'modular' behavior of E. coli CMP kinase is unique in comparison with other NMP kinases.
-Structural and functional consequences of single amino acid substitutions in the pyrimidine base binding pocket of Escherichia coli CMP kinase.,Ofiteru A, Bucurenci N, Alexov E, Bertrand T, Briozzo P, Munier-Lehmann H, Gilles AM FEBS J. 2007 Jul;274(13):3363-73. Epub 2007 Jun 3. PMID:17542990<ref>PMID:17542990</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
@@ Line 35: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Cytidylate kinase]]
 [[Category: Escherichia coli]]
-[[Category: Alexov, E]]
+[[Category: Large Structures]]
-[[Category: Barzu, O]]
+[[Category: Alexov E]]
-[[Category: Bertrand, T]]
+[[Category: Barzu O]]
-[[Category: Briozzo, P]]
+[[Category: Bertrand T]]
-[[Category: Bucurenci, N]]
+[[Category: Briozzo P]]
-[[Category: Gilles, A M]]
+[[Category: Bucurenci N]]
-[[Category: Munier-Lehmann, H]]
+[[Category: Gilles AM]]
-[[Category: Ofiteru, A]]
+[[Category: Munier-Lehmann H]]
-[[Category: Tourneux, L]]
+[[Category: Ofiteru A]]
-[[Category: Nucleotide monophosphate kinase]]
+[[Category: Tourneux L]]
-[[Category: Signaling protein]]
-[[Category: Transferase]]