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| | ==Complex structure of tRNA methyltransferase Trm1 from Aquifex aeolicus with S-adenosyl-L-Methionine== | | ==Complex structure of tRNA methyltransferase Trm1 from Aquifex aeolicus with S-adenosyl-L-Methionine== |
| - | <StructureSection load='3axt' size='340' side='right' caption='[[3axt]], [[Resolution|resolution]] 2.49Å' scene=''> | + | <StructureSection load='3axt' size='340' side='right'caption='[[3axt]], [[Resolution|resolution]] 2.49Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3axt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"aquifex_aeolicus"_huber_and_stetter_2001 "aquifex aeolicus" huber and stetter 2001]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AXT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AXT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3axt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AXT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AXT FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.491Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3axs|3axs]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">trm1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63363 "Aquifex aeolicus" Huber and Stetter 2001])</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=3axt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3axt OCA], [https://pdbe.org/3axt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3axt RCSB], [https://www.ebi.ac.uk/pdbsum/3axt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3axt 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/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216 2.1.1.213, 2.1.1.214, 2.1.1.215 and 2.1.1.216] </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=3axt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3axt OCA], [http://pdbe.org/3axt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3axt RCSB], [http://www.ebi.ac.uk/pdbsum/3axt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3axt ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TRM1_AQUAE TRM1_AQUAE]] Dimethylates the guanine residues at position 26 and 27 of one or more tRNAs using S-adenosyl-L-methionine as donor of the methyl groups.<ref>PMID:19491098</ref> | + | [https://www.uniprot.org/uniprot/TRM1_AQUAE TRM1_AQUAE] Dimethylates the guanine residues at position 26 and 27 of one or more tRNAs using S-adenosyl-L-methionine as donor of the methyl groups.<ref>PMID:19491098</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Aquifex aeolicus huber and stetter 2001]] | |
| - | [[Category: Transferase]] | |
| - | [[Category: Bessho, Y]] | |
| - | [[Category: Ihsanawati]] | |
| - | [[Category: Structural genomic]] | |
| - | [[Category: Sengoku, T]] | |
| - | [[Category: Yokoyama, S]] | |
| | [[Category: Aquifex aeolicus]] | | [[Category: Aquifex aeolicus]] |
| - | [[Category: Guanine 26]] | + | [[Category: Large Structures]] |
| - | [[Category: N2]] | + | [[Category: Bessho Y]] |
| - | [[Category: N2-dimethyltransferase]] | + | [[Category: Ihsanawati]] |
| - | [[Category: Rsgi]] | + | [[Category: Sengoku T]] |
| - | [[Category: Trna modification enzyme]] | + | [[Category: Yokoyama S]] |
| Structural highlights
Function
TRM1_AQUAE Dimethylates the guanine residues at position 26 and 27 of one or more tRNAs using S-adenosyl-L-methionine as donor of the methyl groups.[1]
Publication Abstract from PubMed
Archaeal and eukaryotic tRNA (N(2),N(2)-guanine)-dimethyltransferase (Trm1) produces N(2),N(2)-dimethylguanine at position 26 in tRNA. In contrast, Trm1 from Aquifex aeolicus, a hyper-thermophilic eubacterium, modifies G27 as well as G26. Here, a gel mobility shift assay revealed that the T-arm in tRNA is the binding site of A. aeolicus Trm1. To address the multisite specificity, we performed an x-ray crystal structure study. The overall structure of A. aeolicus Trm1 is similar to that of archaeal Trm1, although there is a zinc-cysteine cluster in the C-terminal domain of A. aeolicus Trm1. The N-terminal domain is a typical catalytic domain of S-adenosyl-l-methionine-dependent methyltransferases. On the basis of the crystal structure and amino acid sequence alignment, we prepared 30 mutant Trm1 proteins. These mutant proteins clarified residues important for S-adenosyl-l-methionine binding and enabled us to propose a hypothetical reaction mechanism. Furthermore, the tRNA-binding site was also elucidated by methyl transfer assay and gel mobility shift assay. The electrostatic potential surface models of A. aeolicus and archaeal Trm1 proteins demonstrated that the distribution of positive charges differs between the two proteins. We constructed a tRNA-docking model, in which the T-arm structure was placed onto the large area of positive charge, which is the expected tRNA-binding site, of A. aeolicus Trm1. In this model, the target G26 base can be placed near the catalytic pocket; however, the nucleotide at position 27 gains closer access to the pocket. Thus, this docking model introduces a rational explanation of the multisite specificity of A. aeolicus Trm1.
Substrate tRNA recognition mechanism of a multisite-specific tRNA methyltransferase, Aquifex aeolicus Trm1, based on the X-ray crystal structure.,Awai T, Ochi A, Ihsanawati, Sengoku T, Hirata A, Bessho Y, Yokoyama S, Hori H J Biol Chem. 2011 Oct 7;286(40):35236-46. Epub 2011 Aug 15. PMID:21844194[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Awai T, Kimura S, Tomikawa C, Ochi A, Ihsanawati, Bessho Y, Yokoyama S, Ohno S, Nishikawa K, Yokogawa T, Suzuki T, Hori H. Aquifex aeolicus tRNA (N2,N2-guanine)-dimethyltransferase (Trm1) catalyzes transfer of methyl groups not only to guanine 26 but also to guanine 27 in tRNA. J Biol Chem. 2009 Jul 31;284(31):20467-78. Epub 2009 Jun 2. PMID:19491098 doi:M109.020024
- ↑ Awai T, Ochi A, Ihsanawati, Sengoku T, Hirata A, Bessho Y, Yokoyama S, Hori H. Substrate tRNA recognition mechanism of a multisite-specific tRNA methyltransferase, Aquifex aeolicus Trm1, based on the X-ray crystal structure. J Biol Chem. 2011 Oct 7;286(40):35236-46. Epub 2011 Aug 15. PMID:21844194 doi:10.1074/jbc.M111.253641
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