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| | ==Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue== | | ==Structure of E. coli 5-Methyluridine Methyltransferase TrmA in complex with 19 nucleotide T-arm analogue== |
| - | <StructureSection load='3bt7' size='340' side='right' caption='[[3bt7]], [[Resolution|resolution]] 2.43Å' scene=''> | + | <StructureSection load='3bt7' size='340' side='right'caption='[[3bt7]], [[Resolution|resolution]] 2.43Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3bt7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BT7 FirstGlance]. <br> | + | <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> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.43Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2bh2|2bh2]], [[1uwv|1uwv]]</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> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">trmA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=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> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/tRNA_(uracil(54)-C(5))-methyltransferase tRNA (uracil(54)-C(5))-methyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.35 2.1.1.35] </span></td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bt7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bt7 OCA], [http://pdbe.org/3bt7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3bt7 RCSB], [http://www.ebi.ac.uk/pdbsum/3bt7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3bt7 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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> | + | [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 == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[TRNA methyltransferase|TRNA methyltransferase]] | + | *[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacillus coli migula 1895]] | + | [[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]]
| + | |
| Structural highlights
Function
TRMA_ECOLI Catalyzes the formation of 5-methyl-uridine at position 54 (m5U54) in all tRNAs.[1] [2]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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 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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ny T, Bjork GR. Cloning and restriction mapping of the trmA gene coding for transfer ribonucleic acid (5-methyluridine)-methyltransferase in Escherichia coli K-12. J Bacteriol. 1980 May;142(2):371-9. PMID:6247318
- ↑ Lindstrom PH, Stuber D, Bjork GR. Genetic organization and transcription from the gene (trmA) responsible for synthesis of tRNA (uracil-5)-methyltransferase by Escherichia coli. J Bacteriol. 1985 Dec;164(3):1117-23. PMID:2999071
- ↑ Alian A, Lee TT, Griner SL, Stroud RM, Finer-Moore J. Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases. Proc Natl Acad Sci U S A. 2008 May 13;105(19):6876-81. Epub 2008 May 1. PMID:18451029
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