3tm5: Difference between revisions

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<StructureSection load='3tm5' size='340' side='right'caption='[[3tm5]], [[Resolution|resolution]] 2.27&Aring;' scene=''>
<StructureSection load='3tm5' size='340' side='right'caption='[[3tm5]], [[Resolution|resolution]] 2.27&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3tm5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TM5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TM5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3tm5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3TM5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3TM5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SFG:SINEFUNGIN'>SFG</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]] 2.27&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3tlj|3tlj]], [[3tm4|3tm4]], [[3tma|3tma]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SFG:SINEFUNGIN'>SFG</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PF1002 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=3tm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tm5 OCA], [https://pdbe.org/3tm5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tm5 RCSB], [https://www.ebi.ac.uk/pdbsum/3tm5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tm5 ProSAT]</span></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=3tm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3tm5 OCA], [https://pdbe.org/3tm5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3tm5 RCSB], [https://www.ebi.ac.uk/pdbsum/3tm5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3tm5 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/TRM14_PYRFU TRM14_PYRFU] S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the methylation of the guanosine nucleotide at position 6 (m2G6) in tRNA(Phe).<ref>PMID:22337946</ref> <ref>PMID:22362751</ref>  
Methyltransferases (MTases) form a major class of tRNA-modifying enzymes needed for the proper functioning of tRNA. Recently, RNA MTases from the TrmN/Trm14 family that are present in Archaea, Bacteria and Eukaryota have been shown to specifically modify tRNA(Phe) at guanosine 6 in the tRNA acceptor stem. Here, we report the first X-ray crystal structures of the tRNA m(2)G6 (N(2)-methylguanosine) MTase (TTC)TrmN from Thermus thermophilus and its ortholog (Pf)Trm14 from Pyrococcus furiosus. Structures of (Pf)Trm14 were solved in complex with the methyl donor S-adenosyl-l-methionine (SAM or AdoMet), as well as the reaction product S-adenosyl-homocysteine (SAH or AdoHcy) and the inhibitor sinefungin. (TTC)TrmN and (Pf)Trm14 consist of an N-terminal THUMP domain fused to a catalytic Rossmann-fold MTase (RFM) domain. These results represent the first crystallographic structure analysis of proteins containing both THUMP and RFM domain, and hence provide further insight in the contribution of the THUMP domain in tRNA recognition and catalysis. Electrostatics and conservation calculations suggest a main tRNA binding surface in a groove between the THUMP domain and the MTase domain. This is further supported by a docking model of TrmN in complex with tRNA(Phe) of T. thermophilus and via site-directed mutagenesis.
 
Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life.,Fislage M, Roovers M, Tuszynska I, Bujnicki JM, Droogmans L, Versees W Nucleic Acids Res. 2012 Feb 22. PMID:22362751<ref>PMID:22362751</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3tm5" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Pyrfu]]
[[Category: Pyrococcus furiosus DSM 3638]]
[[Category: Bujnicki, J M]]
[[Category: Bujnicki JM]]
[[Category: Droogmans, L]]
[[Category: Droogmans L]]
[[Category: Fislage, M]]
[[Category: Fislage M]]
[[Category: Roovers, M]]
[[Category: Roovers M]]
[[Category: Tuszynska, I]]
[[Category: Tuszynska I]]
[[Category: Versees, W]]
[[Category: Versees W]]
[[Category: Methyltransferase]]
[[Category: Rossmann fold]]
[[Category: Thump domain]]
[[Category: Transferase]]
[[Category: Trna methyltransferase]]

Latest revision as of 16:33, 14 March 2024

Crystal structure of Trm14 from Pyrococcus furiosus in complex with sinefunginCrystal structure of Trm14 from Pyrococcus furiosus in complex with sinefungin

Structural highlights

3tm5 is a 2 chain structure with sequence from Pyrococcus furiosus DSM 3638. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.27Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

TRM14_PYRFU S-adenosyl-L-methionine-dependent methyltransferase that catalyzes the methylation of the guanosine nucleotide at position 6 (m2G6) in tRNA(Phe).[1] [2]

See Also

References

  1. ↑ Roovers M, Oudjama Y, Fislage M, Bujnicki JM, Versees W, Droogmans L. The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N(2)-methylguanosine at position 6 in tRNA. RNA. 2012 Apr;18(4):815-24. Epub 2012 Feb 15. PMID:22337946 doi:10.1261/rna.030411.111
  2. ↑ Fislage M, Roovers M, Tuszynska I, Bujnicki JM, Droogmans L, Versees W. Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life. Nucleic Acids Res. 2012 Feb 22. PMID:22362751 doi:10.1093/nar/gks163

3tm5, resolution 2.27Å

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