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| | ==Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-homocysteine== | | ==Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-homocysteine== |
| - | <StructureSection load='3lhd' size='340' side='right' caption='[[3lhd]], [[Resolution|resolution]] 2.59Å' scene=''> | + | <StructureSection load='3lhd' size='340' side='right'caption='[[3lhd]], [[Resolution|resolution]] 2.59Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3lhd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrab Pyrab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LHD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LHD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3lhd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LHD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LHD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 2.59Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3lga|3lga]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PAB0283 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272844 PYRAB])</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=3lhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lhd OCA], [https://pdbe.org/3lhd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lhd RCSB], [https://www.ebi.ac.uk/pdbsum/3lhd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lhd 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=2.1.1.217, 2.1.1.218, 2.1.1.219 and 2.1.1.220 2.1.1.217, 2.1.1.218, 2.1.1.219 and 2.1.1.220] </span></td></tr>
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| - | <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=3lhd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lhd OCA], [http://pdbe.org/3lhd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lhd RCSB], [http://www.ebi.ac.uk/pdbsum/3lhd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lhd ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/TRMI_PYRAB TRMI_PYRAB]] Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenosine at position(s) 57 (m1A57) and 58 (m1A58) in the T-loop of some tRNAs. Methylates the first adenine of an AA sequence.<ref>PMID:14739239</ref> <ref>PMID:20483913</ref> | + | [https://www.uniprot.org/uniprot/TRMI_PYRAB TRMI_PYRAB] Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenosine at position(s) 57 (m1A57) and 58 (m1A58) in the T-loop of some tRNAs. Methylates the first adenine of an AA sequence.<ref>PMID:14739239</ref> <ref>PMID:20483913</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | <jmolCheckbox> | | <jmolCheckbox> |
| | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lh/3lhd_consurf.spt"</scriptWhenChecked> | | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lh/3lhd_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Pyrab]] | + | [[Category: Large Structures]] |
| - | [[Category: Transferase]] | + | [[Category: Pyrococcus abyssi GE5]] |
| - | [[Category: Barbey, C]] | + | [[Category: Barbey C]] |
| - | [[Category: Golinelli-Pimpaneau, B]] | + | [[Category: Golinelli-Pimpaneau B]] |
| - | [[Category: Guelorget, A]] | + | [[Category: Guelorget A]] |
| - | [[Category: Wouters, J]] | + | [[Category: Wouters J]] |
| - | [[Category: Disulfide bond]]
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| - | [[Category: Hyperthermostability]]
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| - | [[Category: Intermolecular contact]]
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| - | [[Category: M1a]]
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| - | [[Category: Methyltransferase]]
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| - | [[Category: Region-specificity]]
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| - | [[Category: Rna methyltransferase]]
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| - | [[Category: Tetramer]]
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| - | [[Category: Trmi]]
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| Structural highlights
Function
TRMI_PYRAB Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenosine at position(s) 57 (m1A57) and 58 (m1A58) in the T-loop of some tRNAs. Methylates the first adenine of an AA sequence.[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
The S-adenosyl-l-methionine dependent methylation of adenine 58 in the T-loop of tRNAs is essential for cell growth in yeast or for adaptation to high temperatures in thermophilic organisms. In contrast to bacterial and eukaryotic tRNA m(1)A58 methyltransferases that are site-specific, the homologous archaeal enzyme from Pyrococcus abyssi catalyzes the formation of m(1)A also at the adjacent position 57, m(1)A57 being a precursor of 1-methylinosine. We report here the crystal structure of P. abyssi tRNA m(1)A57/58 methyltransferase ((Pab)TrmI), in complex with S-adenosyl-l-methionine or S-adenosyl-l-homocysteine in three different space groups. The fold of the monomer and the tetrameric architecture are similar to those of the bacterial enzymes. However, the inter-monomer contacts exhibit unique features. In particular, four disulfide bonds contribute to the hyperthermostability of the archaeal enzyme since their mutation lowers the melting temperature by 16.5 degrees C. His78 in conserved motif X, which is present only in TrmIs from the Thermococcocales order, lies near the active site and displays two alternative conformations. Mutagenesis indicates His78 is important for catalytic efficiency of (Pab)TrmI. When A59 is absent in tRNA(Asp), only A57 is modified. Identification of the methylated positions in tRNAAsp by mass spectrometry confirms that (Pab)TrmI methylates the first adenine of an AA sequence.
Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase.,Guelorget A, Roovers M, Guerineau V, Barbey C, Li X, Golinelli-Pimpaneau B Nucleic Acids Res. 2010 May 18. PMID:20483913[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Roovers M, Wouters J, Bujnicki JM, Tricot C, Stalon V, Grosjean H, Droogmans L. A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res. 2004 Jan 22;32(2):465-76. Print 2004. PMID:14739239 doi:10.1093/nar/gkh191
- ↑ Guelorget A, Roovers M, Guerineau V, Barbey C, Li X, Golinelli-Pimpaneau B. Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase. Nucleic Acids Res. 2010 May 18. PMID:20483913 doi:10.1093/nar/gkq381
- ↑ Guelorget A, Roovers M, Guerineau V, Barbey C, Li X, Golinelli-Pimpaneau B. Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase. Nucleic Acids Res. 2010 May 18. PMID:20483913 doi:10.1093/nar/gkq381
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