3a4t: Difference between revisions

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-{{Seed}}
-[[Image:3a4t.jpg|left|200px]]
-<!--
+==Crystal structure of aTrm4 from M.jannaschii with sinefungin==
-The line below this paragraph, containing "STRUCTURE_3a4t", creates the "Structure Box" on the page.
+<StructureSection load='3a4t' size='340' side='right'caption='[[3a4t]], [[Resolution|resolution]] 2.30&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'>[[3a4t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A4T 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr>
-{{STRUCTURE_3a4t|  PDB=3a4t  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3a4t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a4t OCA], [https://pdbe.org/3a4t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a4t RCSB], [https://www.ebi.ac.uk/pdbsum/3a4t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a4t ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRM4_METJA TRM4_METJA] Catalyzes AdoMet-dependent formation of m5C in tRNA. Cytidine residue at either position 40 or position 48 is likely to be methylated.<ref>PMID:20600111</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/a4/3a4t_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3a4t ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+tRNA:m(5)C methyltransferase Trm4 generates the modified nucleotide 5-methylcytidine in archaeal and eukaryotic tRNA molecules, using S-adenosyl-l-methionine (AdoMet) as methyl donor. Most archaea and eukaryotes possess several Trm4 homologs, including those related to diseases, while the archaeon Methanocaldococcus jannaschii has only one gene encoding a Trm4 homolog, MJ0026. The recombinant MJ0026 protein catalyzed AdoMet-dependent methyltransferase activity on tRNA in vitro and was shown to be the M. jannaschii Trm4. We determined the crystal structures of the substrate-free M. jannaschii Trm4 and its complex with sinefungin at 1.27 A and 2.3 A resolutions, respectively. This AdoMet analog is bound in a negatively charged pocket near helix alpha8. This helix can adopt two different conformations, thereby controlling the entry of AdoMet into the active site. Adjacent to the sinefungin-bound pocket, highly conserved residues form a large, positively charged surface, which seems to be suitable for tRNA binding. The structure explains the roles of several conserved residues that were reportedly involved in the enzymatic activity or stability of Trm4p from the yeast Saccharomyces cerevisiae. We also discuss previous genetic and biochemical data on human NSUN2/hTrm4/Misu and archaeal PAB1947 methyltransferase, based on the structure of M. jannaschii Trm4.
-===Crystal structure of aTrm4 from M.jannaschii with sinefungin===
+Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin.,Kuratani M, Hirano M, Goto-Ito S, Itoh Y, Hikida Y, Nishimoto M, Sekine S, Bessho Y, Ito T, Grosjean H, Yokoyama S J Mol Biol. 2010 Aug 20;401(3):323-33. Epub 2010 Jun 30. PMID:20600111<ref>PMID:20600111</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-A4T is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii Methanocaldococcus jannaschii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A4T OCA].
+<div class="pdbe-citations 3a4t" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Methanocaldococcus jannaschii]]
-[[Category: Hirano, M.]]
+[[Category: Hirano M]]
-[[Category: Kuratani, M.]]
+[[Category: Kuratani M]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S.]]
-[[Category: M5c]]
-[[Category: Methyltransferase]]
-[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: Rossmann fold]]
-[[Category: Rsgi]]
-[[Category: S-adenosyl-l-methionine]]
-[[Category: Structural genomic]]
-[[Category: Transferase]]
-[[Category: Trna]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 30 13:45:31 2010''