1nv8: Difference between revisions

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OCA

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-[[Image:1nv8.gif|left|200px]]<br /><applet load="1nv8" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1nv8, resolution 2.20&Aring;" />
-'''N5-glutamine methyltransferase, HemK'''<br />
-==Overview==
+==N5-glutamine methyltransferase, HemK==
-Posttranslational methylation of release factors on the glutamine residue, of a conserved GGQ motif is required for efficient termination of protein, synthesis. This methylation is performed by an N(5)-glutamine, methyltransferase called PrmC/HemK, whose crystal structure we report here, at 2.2 A resolution. The electron density at the active site appears to, contain a mixture of the substrates, S-adenosyl-L-methionine (AdoMet) and, glutamine, and the products, S-adenosyl-L-homocysteine (AdoHcy) and, N(5)-methylglutamine. The C-terminal domain of PrmC adopts the canonical, AdoMet-dependent methyltransferase fold and shares structural similarity, with the nucleotide N-methyltransferases in the active site, including use, of a conserved (D/N)PPY motif to select and position the glutamine, substrate. Residues of the PrmC (197)NPPY(200) motif form hydrogen bonds, that position the planar Gln side chain such that the lone-pair electrons, on the nitrogen nucleophile are oriented toward the methyl group of, AdoMet. In the product complex, the methyl group remains pointing toward, the sulfur, consistent with either an sp(3)-hybridized, positively charged, Gln nitrogen, or a neutral sp(2)-hybridized nitrogen in a strained, conformation. Due to steric overlap within the active site, proton loss, and formation of the neutral planar methylamide product are likely to, occur during or after product release. These structures, therefore, represent intermediates along the catalytic pathway of PrmC and show how, the (D/N)PPY motif can be used to select a wide variety substrates.
+<StructureSection load='1nv8' size='340' side='right'caption='[[1nv8]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1nv8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NV8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NV8 FirstGlance]. <br>
-NV8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] with SAM and MEQ as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NV8 OCA].
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MEQ:N5-METHYLGLUTAMINE'>MEQ</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
-==Reference==
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1nv8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nv8 OCA], [https://pdbe.org/1nv8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nv8 RCSB], [https://www.ebi.ac.uk/pdbsum/1nv8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nv8 ProSAT]</span></td></tr>
-Structures along the catalytic pathway of PrmC/HemK, an N5-glutamine AdoMet-dependent methyltransferase., Schubert HL, Phillips JD, Hill CP, Biochemistry. 2003 May 20;42(19):5592-9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12741815 12741815]
+</table>
-[[Category: Single protein]]
+== Function ==
+[https://www.uniprot.org/uniprot/PRMC_THEMA PRMC_THEMA] Methylates the class 1 translation termination release factors RF1/PrfA and RF2/PrfB on the glutamine residue of the universally conserved GGQ motif.
+== 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/nv/1nv8_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=1nv8 ConSurf].
+<div style="clear:both"></div>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermotoga maritima]]
-[[Category: Hill, C.P.]]
+[[Category: Hill CP]]
-[[Category: Phillips, J.D.]]
+[[Category: Phillips JD]]
-[[Category: Schubert, H.L.]]
+[[Category: Schubert HL]]
-[[Category: MEQ]]
-[[Category: SAM]]
-[[Category: class i adomet-dependent methyltransferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 23:51:42 2007''