1bky: Difference between revisions

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-[[Image:1bky.gif|left|200px]]
-<!--
+==VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1CYT AND S-ADENOSYLHOMOCYSTEINE==
-The line below this paragraph, containing "STRUCTURE_1bky", creates the "Structure Box" on the page.
+<StructureSection load='1bky' size='340' side='right'caption='[[1bky]], [[Resolution|resolution]] 2.00&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'>[[1bky]] 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=1BKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BKY 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]] 2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MC:1-METHYLCYTOSINE'>1MC</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-{{STRUCTURE_1bky|  PDB=1bky  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bky OCA], [https://pdbe.org/1bky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bky RCSB], [https://www.ebi.ac.uk/pdbsum/1bky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bky ProSAT]</span></td></tr>
+</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/bk/1bky_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=1bky ConSurf].
+<div style="clear:both"></div>
-'''VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M1CYT AND S-ADENOSYLHOMOCYSTEINE'''
+==See Also==
+*[[Poly(A) polymerase 3D structures|Poly(A) polymerase 3D structures]]
+== References ==
-==Overview==
+<references/>
-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.
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-BKY is a [[Single protein]] structure of 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=1BKY OCA].
-==Reference==
-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:[http://www.ncbi.nlm.nih.gov/pubmed/10377383 10377383]
-[[Category: Polynucleotide adenylyltransferase]]
-[[Category: Single protein]]
 [[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 cytosine]]
-[[Category: Methyltransferase]]
-[[Category: Mrna processing]]
-[[Category: Rna cap analog]]
-[[Category: Transcription]]
-[[Category: Vaccinia]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 11:38:50 2008''