2YY8

Crystal structure of archaeal tRNA-methylase for position 56 (aTrm56) from Pyrococcus horikoshii, complexed with S-adenosyl-L-methionine

Summary for 2YY8

• Entry DOI: 10.2210/pdb2yy8/pdb
• Descriptor: UPF0106 protein PH0461, 5'-DEOXY-5'-METHYLTHIOADENOSINE, S-ADENOSYLMETHIONINE, ... (4 entities in total)
• Functional Keywords: deep trefoil knot, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, transferase
• Biological source: Pyrococcus horikoshii
• Cellular location: Cytoplasm (Potential): O58214
• Total number of polymer chains: 2
• Total formula weight: 46414.54

Authors

Kuratani, M.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2007-04-27, release date: 2008-03-18, Last modification date: 2024-03-13)

Primary citation

Kuratani, M.,Bessho, Y.,Nishimoto, M.,Grosjean, H.,Yokoyama, S.
Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2'-O-methylcytidine at position 56 of tRNA
J.Mol.Biol., 375:1064-1075, 2008

PubMed Abstract: The conserved cytidine residue at position 56 of tRNA contributes to the maintenance of the L-shaped tertiary structure. aTrm56 catalyzes the 2'-O-methylation of the cytidine residue in archaeal tRNA, using S-adenosyl-L-methionine. Based on the amino acid sequence, aTrm56 is the most distant member of the SpoU family. Here, we determined the crystal structure of Pyrococcus horikoshii aTrm56 complexed with S-adenosyl-L-methionine at 2.48 A resolution. aTrm56 consists of the SPOUT domain, which contains the characteristic deep trefoil knot, and a unique C-terminal beta-hairpin. aTrm56 forms a dimer. The S-adenosyl-L-methionine binding and dimerization of aTrm56 were similar to those of the other SpoU members. A structure-based sequence alignment revealed that aTrm56 conserves only motif II, among the four signature motifs. However, an essential Arg16 residue is located at a novel position within motif I. Biochemical assays showed that aTrm56 prefers the L-shaped tRNA to the lambda form as its substrate.

PubMed: 18068186
DOI: 10.1016/j.jmb.2007.11.023

Experimental method

X-RAY DIFFRACTION (2.48 Å)