1b42: Difference between revisions

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 ==VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1ADE AND S-ADENOSYLHOMOCYSTEINE==
-<StructureSection load='1b42' size='340' side='right' caption='[[1b42]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+<StructureSection load='1b42' size='340' side='right'caption='[[1b42]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1b42]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1B42 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1b42]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vaccinia_virus Vaccinia virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B42 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=M1A:6-AMINO-1-METHYLPURINE'>M1A</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>
+</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><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Polynucleotide_adenylyltransferase Polynucleotide adenylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.19 2.7.7.19] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M1A:6-AMINO-1-METHYLPURINE'>M1A</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1b42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b42 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1b42 RCSB], [http://www.ebi.ac.uk/pdbsum/1b42 PDBsum]</span></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=1b42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b42 OCA], [https://pdbe.org/1b42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b42 RCSB], [https://www.ebi.ac.uk/pdbsum/1b42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b42 ProSAT]</span></td></tr>
-<table>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/MCE_VACCW MCE_VACCW] Displays methyltransferase, positive regulation of the poly(A) polymerase and transcription elongation activities. Involved in the modification of both mRNA ends and in intermediate and late gene positive transcription elongation. At the mRNAs 5' end, methylates the ribose 2' OH group of the first transcribed nucleotide, thereby producing a 2'-O-methylpurine cap. At the 3' end, functions as a processivity factor which stimulates the activity of the viral poly(A) polymerase VP55 that creates mRNA's poly(A) tail. In the presence of VP39, VP55 does not dissociate from the RNA allowing tail elongation to around 250 adenylates.<ref>PMID:1313572</ref> <ref>PMID:1670500</ref> <ref>PMID:12359447</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/b4/1b42_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b4/1b42_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=1b42 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-We have determined, by high resolution x-ray analysis, 10 structures comprising the mRNA cap-specific methyltransferase VP39 or specific mutants thereof in the presence of methylated nucleobase analogs (N1-methyladenine, N3-methyladenine, N1-methylcytosine, N3-methylcytosine) and their unmethylated counterparts, or nucleoside N7-methylguanosine. Together with solution affinity studies and previous crystallographic data for N7-methylguanosine and its phosphorylated derivatives, these data demonstrate that only methylated, positively charged bases are bound, indicating that their enhanced stacking with two aromatic side chains of VP39 (Tyr 22 and Phe 180) plays a dominant role in cap recognition. Four key features characterize this stacking interaction: (i) near perfect parallel alignment between the sandwiched methylated bases and aromatic side chains, (ii) substantial areas of overlap in the two-stacked rings, (iii) a 3.4-A interplanar spacing within the overlapping region, and (iv) positive charge in the heterocyclic nucleobase.
-mRNA cap recognition: dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains.,Hu G, Gershon PD, Hodel AE, Quiocho FA Proc Natl Acad Sci U S A. 1999 Jun 22;96(13):7149-54. PMID:10377383<ref>PMID:10377383</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Poly(A) Polymerase|Poly(A) Polymerase]]
+*[[Poly(A) polymerase 3D structures|Poly(A) polymerase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Polynucleotide adenylyltransferase]]
+[[Category: Large Structures]]
 [[Category: Vaccinia virus]]
-[[Category: Gershon, P D.]]
+[[Category: Gershon PD]]
-[[Category: Hodel, A E.]]
+[[Category: Hodel AE]]
-[[Category: Hu, G.]]
+[[Category: Hu G]]
-[[Category: Quiocho, F A.]]
+[[Category: Quiocho FA]]
-[[Category: Methylated adenine]]
-[[Category: Methyltransferase]]
-[[Category: Mrna processing]]
-[[Category: Rna cap analog]]
-[[Category: Transcription]]
-[[Category: Vaccinia]]