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| - | [[Image:2pwy.jpg|left|200px]] | |
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| - | <!-- | + | ==Crystal Structure of a m1A58 tRNA methyltransferase== |
| - | The line below this paragraph, containing "STRUCTURE_2pwy", creates the "Structure Box" on the page.
| + | <StructureSection load='2pwy' size='340' side='right'caption='[[2pwy]], [[Resolution|resolution]] 1.70Å' 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'>[[2pwy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB27 Thermus thermophilus HB27]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PWY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PWY 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]] 1.7Å</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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | {{STRUCTURE_2pwy| PDB=2pwy | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pwy OCA], [https://pdbe.org/2pwy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pwy RCSB], [https://www.ebi.ac.uk/pdbsum/2pwy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pwy ProSAT]</span></td></tr> |
| | + | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/TRMI_THET2 TRMI_THET2] Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 58 (m1A58) in tRNA. Is required for cell growth at extreme temperatures.<ref>PMID:12682365</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/pw/2pwy_consurf.spt"</scriptWhenChecked> |
| | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2pwy ConSurf]. |
| | + | <div style="clear:both"></div> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Methyltransferases from the m(1)A(58) tRNA methyltransferase (TrmI) family catalyze the S-adenosyl-l-methionine-dependent N(1)-methylation of tRNA adenosine 58. The crystal structure of Thermus thermophilus TrmI, in complex with S-adenosyl-l-homocysteine, was determined at 1.7 A resolution. This structure is closely related to that of Mycobacterium tuberculosis TrmI, and their comparison enabled us to enlighten two grooves in the TrmI structure that are large enough and electrostatically compatible to accommodate one tRNA per face of TrmI tetramer. We have then conducted a biophysical study based on electrospray ionization mass spectrometry, site-directed mutagenesis, and molecular docking. First, we confirmed the tetrameric oligomerization state of TrmI, and we showed that this protein remains tetrameric upon tRNA binding, with formation of complexes involving one to two molecules of tRNA per TrmI tetramer. Second, three key residues for the methylation reaction were identified: the universally conserved D170 and two conserved aromatic residues Y78 and Y194. We then used molecular docking to position a N(9)-methyladenine in the active site of TrmI. The N(9)-methyladenine snugly fits into the catalytic cleft, where the side chain of D170 acts as a bidentate ligand binding the amino moiety of S-adenosyl-l-methionine and the exocyclic amino group of the adenosine. Y194 interacts with the N(9)-methyladenine ring, whereas Y78 can stabilize the sugar ring. From our results, we propose that the conserved residues that form the catalytic cavity (D170, Y78, and Y194) are essential for fashioning an optimized shape of the catalytic pocket. |
| | | | |
| - | '''Crystal Structure of a m1A58 tRNA methyltransferase'''
| + | Crystal structure of Thermus thermophilus tRNA m1A58 methyltransferase and biophysical characterization of its interaction with tRNA.,Barraud P, Golinelli-Pimpaneau B, Atmanene C, Sanglier S, Van Dorsselaer A, Droogmans L, Dardel F, Tisne C J Mol Biol. 2008 Mar 21;377(2):535-50. Epub 2008 Jan 26. PMID:18262540<ref>PMID:18262540</ref> |
| - | | + | |
| - | | + | |
| - | ==Overview==
| + | |
| - | Methyltransferases from the m(1)A(58) tRNA methyltransferase (TrmI) family catalyze the S-adenosyl-l-methionine-dependent N(1)-methylation of tRNA adenosine 58. The crystal structure of Thermus thermophilus TrmI, in complex with S-adenosyl-l-homocysteine, was determined at 1.7 A resolution. This structure is closely related to that of Mycobacterium tuberculosis TrmI, and their comparison enabled us to enlighten two grooves in the TrmI structure that are large enough and electrostatically compatible to accommodate one tRNA per face of TrmI tetramer. We have then conducted a biophysical study based on electrospray ionization mass spectrometry, site-directed mutagenesis, and molecular docking. First, we confirmed the tetrameric oligomerization state of TrmI, and we showed that this protein remains tetrameric upon tRNA binding, with formation of complexes involving one to two molecules of tRNA per TrmI tetramer. Second, three key residues for the methylation reaction were identified: the universally conserved D170 and two conserved aromatic residues Y78 and Y194. We then used molecular docking to position a N(9)-methyladenine in the active site of TrmI. The N(9)-methyladenine snugly fits into the catalytic cleft, where the side chain of D170 acts as a bidentate ligand binding the amino moiety of S-adenosyl-l-methionine and the exocyclic amino group of the adenosine. Y194 interacts with the N(9)-methyladenine ring, whereas Y78 can stabilize the sugar ring. From our results, we propose that the conserved residues that form the catalytic cavity (D170, Y78, and Y194) are essential for fashioning an optimized shape of the catalytic pocket.
| + | |
| | | | |
| - | ==About this Structure==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | 2PWY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PWY OCA].
| + | </div> |
| | + | <div class="pdbe-citations 2pwy" style="background-color:#fffaf0;"></div> |
| | | | |
| - | ==Reference== | + | ==See Also== |
| - | Crystal Structure of Thermus thermophilus tRNA m(1)A(58) Methyltransferase and Biophysical Characterization of Its Interaction with tRNA., Barraud P, Golinelli-Pimpaneau B, Atmanene C, Sanglier S, Van Dorsselaer A, Droogmans L, Dardel F, Tisne C, J Mol Biol. 2008 Jan 26;. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18262540 18262540]
| + | *[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]] |
| - | [[Category: Single protein]] | + | == References == |
| - | [[Category: Thermus thermophilus]] | + | <references/> |
| - | [[Category: Barraud, P.]] | + | __TOC__ |
| - | [[Category: Golinelli-Pimpaneau, B.]] | + | </StructureSection> |
| - | [[Category: Tisne, C.]] | + | [[Category: Large Structures]] |
| - | [[Category: Adomet]]
| + | [[Category: Thermus thermophilus HB27]] |
| - | [[Category: Mtase]]
| + | [[Category: Barraud P]] |
| - | [[Category: Transferase]]
| + | [[Category: Golinelli-Pimpaneau B]] |
| - | [[Category: Trmi]]
| + | [[Category: Tisne C]] |
| - | [[Category: Trna-m1a58]]
| + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 13:56:16 2008''
| + | |
| Structural highlights
Function
TRMI_THET2 Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 58 (m1A58) in tRNA. Is required for cell growth at extreme temperatures.[1]
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
Methyltransferases from the m(1)A(58) tRNA methyltransferase (TrmI) family catalyze the S-adenosyl-l-methionine-dependent N(1)-methylation of tRNA adenosine 58. The crystal structure of Thermus thermophilus TrmI, in complex with S-adenosyl-l-homocysteine, was determined at 1.7 A resolution. This structure is closely related to that of Mycobacterium tuberculosis TrmI, and their comparison enabled us to enlighten two grooves in the TrmI structure that are large enough and electrostatically compatible to accommodate one tRNA per face of TrmI tetramer. We have then conducted a biophysical study based on electrospray ionization mass spectrometry, site-directed mutagenesis, and molecular docking. First, we confirmed the tetrameric oligomerization state of TrmI, and we showed that this protein remains tetrameric upon tRNA binding, with formation of complexes involving one to two molecules of tRNA per TrmI tetramer. Second, three key residues for the methylation reaction were identified: the universally conserved D170 and two conserved aromatic residues Y78 and Y194. We then used molecular docking to position a N(9)-methyladenine in the active site of TrmI. The N(9)-methyladenine snugly fits into the catalytic cleft, where the side chain of D170 acts as a bidentate ligand binding the amino moiety of S-adenosyl-l-methionine and the exocyclic amino group of the adenosine. Y194 interacts with the N(9)-methyladenine ring, whereas Y78 can stabilize the sugar ring. From our results, we propose that the conserved residues that form the catalytic cavity (D170, Y78, and Y194) are essential for fashioning an optimized shape of the catalytic pocket.
Crystal structure of Thermus thermophilus tRNA m1A58 methyltransferase and biophysical characterization of its interaction with tRNA.,Barraud P, Golinelli-Pimpaneau B, Atmanene C, Sanglier S, Van Dorsselaer A, Droogmans L, Dardel F, Tisne C J Mol Biol. 2008 Mar 21;377(2):535-50. Epub 2008 Jan 26. PMID:18262540[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Droogmans L, Roovers M, Bujnicki JM, Tricot C, Hartsch T, Stalon V, Grosjean H. Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Nucleic Acids Res. 2003 Apr 15;31(8):2148-56. PMID:12682365
- ↑ Barraud P, Golinelli-Pimpaneau B, Atmanene C, Sanglier S, Van Dorsselaer A, Droogmans L, Dardel F, Tisne C. Crystal structure of Thermus thermophilus tRNA m1A58 methyltransferase and biophysical characterization of its interaction with tRNA. J Mol Biol. 2008 Mar 21;377(2):535-50. Epub 2008 Jan 26. PMID:18262540 doi:10.1016/j.jmb.2008.01.041
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