3bt7: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3bt7.png|left|200px]]
-<!--
+==Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue==
-The line below this paragraph, containing "STRUCTURE_3bt7", creates the "Structure Box" on the page.
+<StructureSection load='3bt7' size='340' side='right'caption='[[3bt7]], [[Resolution|resolution]] 2.43&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'>[[3bt7]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BT7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BT7 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]] 2.43&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene></td></tr>
-{{STRUCTURE_3bt7|  PDB=3bt7  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3bt7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bt7 OCA], [https://pdbe.org/3bt7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bt7 RCSB], [https://www.ebi.ac.uk/pdbsum/3bt7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bt7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/TRMA_ECOLI TRMA_ECOLI] Catalyzes the formation of 5-methyl-uridine at position 54 (m5U54) in all tRNAs.<ref>PMID:6247318</ref> <ref>PMID:2999071</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/bt/3bt7_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=3bt7 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+TrmA catalyzes S-adenosylmethionine (AdoMet)-dependent methylation of U54 in most tRNAs. We solved the structure of the Escherichia coli 5-methyluridine (m(5)U) 54 tRNA methyltransferase (MTase) TrmA in a covalent complex with a 19-nt T arm analog to 2.4-A resolution. Mutation of the TrmA catalytic base Glu-358 to Gln arrested catalysis and allowed isolation of the covalent TrmA-RNA complex for crystallization. The protein-RNA interface includes 6 nt of the T loop and two proximal base pairs of the stem. U54 is flipped out of the loop into the active site. A58 occupies the space of the everted U54 and is part of a collinear base stack G53-A58-G57-C56-U55. The RNA fold is different from T loop conformations in unbound tRNA or T arm analogs, but nearly identical to the fold of the RNA loop bound at the active site of the m(5)U MTase RumA. In both enzymes, this consensus fold presents the target U and the following two bases to a conserved binding groove on the protein. Outside of this fold, the RumA and TrmA substrates have completely different structures and protein interfaces. Loop residues other than the target U54 make more than half of their hydrogen bonds to the protein via sugar-phosphate moieties, accounting, in part, for the broad consensus sequence for TrmA substrates.
-===Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue===
+Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases.,Alian A, Lee TT, Griner SL, Stroud RM, Finer-Moore J Proc Natl Acad Sci U S A. 2008 May 13;105(19):6876-81. Epub 2008 May 1. PMID:18451029<ref>PMID:18451029</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3bt7" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18451029}}, adds the Publication Abstract to the page
+*[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18451029 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18451029}}
+__TOC__
+</StructureSection>
-==About this Structure==
-BT7 is a 4 chains structure of sequences 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=3BT7 OCA].
-==Reference==
-<ref group="xtra">PMID:18451029</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: Alian, A.]]
+[[Category: Large Structures]]
-[[Category: Finer-Moore, J.]]
+[[Category: Synthetic construct]]
-[[Category: Stroud, R M.]]
+[[Category: Alian A]]
-[[Category: Methyltransferase]]
+[[Category: Finer-Moore J]]
-[[Category: Methyluridine]]
+[[Category: Stroud RM]]
-[[Category: Rumt]]
-[[Category: S-adenosyl-l-methionine]]
-[[Category: Transferase/rna complex]]
-[[Category: Trma]]
-[[Category: Trna processing]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 21:23:19 2009''