3TMA

Crystal structure of TrmN from Thermus thermophilus

Summary for 3TMA

• Entry DOI: 10.2210/pdb3tma/pdb
• Related: 3TLJ 3TM4 3TM5
• Descriptor: methyltransferase, PHOSPHATE ION (3 entities in total)
• Functional Keywords: rossmann fold methyltransferase, thump domain, trna methyltransferase, transferase
• Biological source: Thermus thermophilus
• Total number of polymer chains: 1
• Total formula weight: 39173.12

Authors

Fislage, M.,Roovers, M.,Tuszynska, I.,Bujnicki, J.M.,Droogmans, L.,Versees, W. (deposition date: 2011-08-31, release date: 2012-03-14, Last modification date: 2023-09-13)

Primary citation

Fislage, M.,Roovers, M.,Tuszynska, I.,Bujnicki, J.M.,Droogmans, L.,Versees, W.
Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life.
Nucleic Acids Res., 40:5149-5161, 2012

PubMed Abstract: 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.

PubMed: 22362751
DOI: 10.1093/nar/gks163

Experimental method

X-RAY DIFFRACTION (2.05 Å)