PDBsum entry: 2dul

Transferase

PDB id: 2dul

Contents

Protein chain

367 a.a. *

Ligands

GOL

Waters ×320

* Residue conservation analysis

PDB id:

2dul

Name:

Transferase

Title:

Crystal structure of tRNA g26 methyltransferase trm1 in apo pyrococcus horikoshii

Structure:

N(2),n(2)-dimethylguanosine tRNA methyltransferas chain: a. Fragment: residues 1-378. Synonym: tRNA(guanine-26,n(2)-n(2)) methyltransferase, tRNA dimethylguanosine-26 methyltransferase, tRNA(m(2,2)g26) dimethyltransferase. Engineered: yes. Mutation: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 53953. Gene: trm1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.90Å R-factor: 0.195 R-free: 0.227

Authors:

Ihsanawati,M.Shirouzu,Y.Bessho,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

Ihsanawati et al. (2008). Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii. J Mol Biol, 383, 871-884. PubMed id: 18789948 DOI: 10.1016/j.jmb.2008.08.068

Date:

24-Jul-06 Release date: 24-Jan-07

Protein chain

O59493  (TRM1_PYRHO) -  tRNA (guanine(26)-N(2))-dimethyltransferase

Seq: 381 a.a.

Struc: 367 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.216 - tRNA (guanine(26)-N(2))-dimethyltransferase.
• Reaction: 2 S-adenosyl-L-methionine + guanine₂₆ in tRNA = 2 S-adenosyl-L- homocysteine + N₂-dimethylguanine₂₆ in tRNA

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: methylation (2 terms)
• Biochemical function: transferase activity (4 terms)

Added reference

DOI no: 10.1016/j.jmb.2008.08.068

J Mol Biol 383:871-884 (2008)

PubMed id: 18789948

Crystal structure of tRNA N2,N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii.

Ihsanawati, M.Nishimoto, K.Higashijima, M.Shirouzu, H.Grosjean, Y.Bessho, S.Yokoyama.

ABSTRACT

Trm1 catalyzes a two-step reaction, leading to mono- and dimethylation of guanosine at position 26 in most eukaryotic and archaeal tRNAs. We report the crystal structures of Trm1 from Pyrococcus horikoshii liganded with S-adenosyl-l-methionine or S-adenosyl-l-homocysteine. The protein comprises N-terminal and C-terminal domains with class I methyltransferase and novel folds, respectively. The methyl moiety of S-adenosyl-l-methionine points toward the invariant Phe27 and Phe140 within a narrow pocket, where the target G26 might flip in. Mutagenesis of Phe27 or Phe140 to alanine abolished the enzyme activity, indicating their role in methylating G26. Structural analyses revealed that the movements of Phe140 and the loop preceding Phe27 may be involved in dissociation of the monomethylated tRNA*Trm1 complex prior to the second methylation. Moreover, the catalytic residues Asp138, Pro139, and Phe140 are in a different motif from that in DNA 6-methyladenosine methyltransferases, suggesting a different methyl transfer mechanism in the Trm1 family.

Selected figure(s)

Figure 1.
Fig. 1. A schematic drawing of the two-step reaction for the formation of m^2G and m^2[2]G in tRNAs.^6 Free rotation of the bond between the purine ring and the exocyclic nitrogen, which occurs easily in solution, is indicated by an arrow.

Figure 7.
Fig. 7. Proposed reaction mechanisms of P. horikoshii Trm1. (a) A stereo view of a superimposition of the DPF sequence of P. horikoshii Trm1 (brown) with the DPPY motifs of mono-MTases [DNA N^6-adenine (magenta) and rRNA N^2-guanosine (green)] and a di-MTase [bacterial ErmC (yellow)]. (b) A schematic drawing of the proposed methyl transfer mechanism. In P. horikoshii Trm1, D138 may act as a base to deprotonate one hydrogen atom of the exocyclic amino group of G26. The exocyclic amino group of G26 thus becomes a nucleophile, stabilized by π–π stacking of Phe27, and ready to attack the methyl group of AdoMet.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 383, 871-884) copyright 2008.

Figures were selected by an automated process.