Crystal Structure of tRNA N2,N2-Guanosine Dimethyltransferase Trm1 from Pyrococcus horikoshii

Ihsanawati,; Nishimoto, Madoka; Higashijima, Kyoko; Shirouzu, Mikako; Grosjean, Henri; Bessho, Yoshitaka; Yokoyama, Shigeyuki

doi:10.1016/j.jmb.2008.08.068

Cited by 31 publications

(48 citation statements)

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“…For example, the local RNA structure recognition is commonly observed in tRNA (⌿55) synthase (28), tRNA guanine transglycosidase (29), tRNA (Gm18) methyltransferase (30,31), tRNA (m 1 G37) methyltransferase (32), tRNA (m 7 G46) methyltransferase (33), tRNA (i 6 A37) isopentenyltransferase (34,35), and others. The single displacement methyl transfer mechanism is common to at least tRNA (m (36,37) and tRNA (Gm18) methyltransferase (38,39). Furthermore, the eukaryotic enzyme was identified from Saccharomyces cerevisiae as Trm2 (39 -41).…”

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confidence: 99%

The tRNA Recognition Mechanism of Folate/FAD-dependent tRNA Methyltransferase (TrmFO)

Yamagami

Yamashita

Nishimasu

et al. 2012

Journal of Biological Chemistry

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Background: RNA modification enzymes select specific RNAs as substrates. Results: A novel assay for folate-dependent tRNA methyltransferase (TrmFO) was developed that clarified positive and negative determinants of TrmFO. Conclusion: TrmFO recognizes a T-arm structure including the U54U55C56 sequence and G53-C61 base pair; A38 prevents incorrect methylation of U32. Significance: Studying how proteins recognize RNA is crucial for understanding RNA maturation processes.

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confidence: 99%

The tRNA Recognition Mechanism of Folate/FAD-dependent tRNA Methyltransferase (TrmFO)

Yamagami

Yamashita

Nishimasu

et al. 2012

Journal of Biological Chemistry

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“…The enzymes responsible for these methylations have been extensively studied, including the determination of the structure for an archaeal Trm1 enzyme that forms m 2 2 G26 (Ihsanawati et al 2008). In contrast, m 2 G is rather scarce in bacterial tRNA.…”

Section: Discussionmentioning

confidence: 99%

“…These dimethylations are catalyzed by two distinct MTases. Biochemical (Constantinesco et al 1998) as well as structural (Ihsanawati et al 2008) studies were performed with the Trm1 enzyme of the hyperthermophilic euryarchaeon Pyrococcus furiosus. The Pf Trm1 enzyme needs specific base-pairing in the D-loop, limited size of the variable loop, and a correct overall tRNA folding for N 2 ,N 2 -dimethylation of G26 (Constantinesco et al 1999).…”

Section: Introductionmentioning

confidence: 99%

The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N²-methylguanosine at position 6 in tRNA

Roovers¹,

Oudjama²,

Fislage³

et al. 2012

RNA

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N 2 -methylguanosine (m 2 G) is found at position 6 in the acceptor stem of Thermus thermophilus tRNA Phe . In this article, we describe the cloning, expression, and characterization of the T. thermophilus HB27 methyltransferase (MTase) encoded by the TTC1157 open reading frame that catalyzes the formation of this modified nucleoside. S-adenosyl-L-methionine is used as donor of the methyl group. The enzyme behaves as a monomer in solution. It contains an N-terminal THUMP domain predicted to bind RNA and contains a C-terminal Rossmann-fold methyltransferase (RFM) domain predicted to be responsible for catalysis. We propose to rename the TTC1157 gene trmN and the corresponding protein TrmN, according to the bacterial nomenclature of tRNA methyltransferases. Inactivation of the trmN gene in the T. thermophilus HB27 chromosome led to a total absence of m 2 G in tRNA but did not affect cell growth or the formation of other modified nucleosides in tRNA Phe . Archaeal homologs of TrmN were identified and characterized. These proteins catalyze the same reaction as TrmN from T. thermophilus. Individual THUMP and RFM domains of PF1002 from Pyrococcus furiosus were produced. These separate domains were inactive and did not bind tRNA, reinforcing the idea that the THUMP domain acts in concert with the catalytic domain to target a particular position of the tRNA molecule.

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“…3, cyan), and a C-terminal novel structure domain (magenta). Although the C-terminal domain structure of A. aeolicus Trm1 is clearly different from that of P. horikoshii Trm1 (archaeal enzyme; PDB codes 2EJT and 2DUL) (19), the overall structure and topology of A. aeolicus Trm1 is similar to that of P. horikoshii Trm1 (Fig. 4).…”

Section: A Aeolicus Trm1 Recognizes the T-arm Structure In Trna-mentioning

confidence: 97%

“…The most highly purified enzyme from a native source was obtained from Tetrahymena pyriformis (4). The responsible gene was first determined to be trm1 from Saccharomyces cerevisiae (13,14) and then experimentally identified from various eukaryotes (Schizosaccharomyces pombe (15), Caenorhabditis elegans (16), and human (17)) and archaea (Pyrococcus furiosus (18), Pyrococcus horikoshii (19), and Haloferax volcanii (20)), consistent with the distribution of the m 2 2 G26 (or m 2 G26) modification in tRNA. Furthermore, we have recently reported that Aquifex aeolicus, a hyper-thermophilic eubacterium, has a Trm1 protein that catalyzes methyl transfer not only to G26 but also to G27 (21).…”

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confidence: 88%

Substrate tRNA Recognition Mechanism of a Multisite-specific tRNA Methyltransferase, Aquifex aeolicus Trm1, Based on the X-ray Crystal Structure

Awai

Ochi

Ihsanawati

et al. 2011

Journal of Biological Chemistry

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Archaeal and eukaryotic tRNA (N 2 ,N 2 -guanine)-dimethyltransferase (Trm1) produces N 2 ,N 2 -dimethylguanine at position 26 in tRNA. In contrast, Trm1 from Aquifex aeolicus, a hyper-thermophilic eubacterium, modifies G27 as well as G26. Here, a gel mobility shift assay revealed that the T-arm in tRNA is the binding site of A. aeolicus Trm1. To address the multisite specificity, we performed an x-ray crystal structure study. The overall structure of A. aeolicus Trm1 is similar to that of archaeal Trm1, although there is a zinc-cysteine cluster in the C-terminal domain of A. aeolicus Trm1. The N-terminal domain is a typical catalytic domain of S-adenosyl-L-methionine-dependent methyltransferases. On the basis of the crystal structure and amino acid sequence alignment, we prepared 30 mutant Trm1 proteins. These mutant proteins clarified residues important for S-adenosyl-L-methionine binding and enabled us to propose a hypothetical reaction mechanism. Furthermore, the tRNA-binding site was also elucidated by methyl transfer assay and gel mobility shift assay. The electrostatic potential surface models of A. aeolicus and archaeal Trm1 proteins demonstrated that the distribution of positive charges differs between the two proteins. We constructed a tRNA-docking model, in which the T-arm structure was placed onto the large area of positive charge, which is the expected tRNA-binding site, of A. aeolicus Trm1. In this model, the target G26 base can be placed near the catalytic pocket; however, the nucleotide at position 27 gains closer access to the pocket. Thus, this docking model introduces a rational explanation of the multisite specificity of A. aeolicus Trm1.Methylation is one of the most common chemical modifications that occurs in a broad range of biomolecules, including nucleic acids, proteins, lipids, and small compounds. It is implicated in a variety of cellular processes, such as translation, transcription, processing of RNA, epigenetics, development, carcinogenesis, neurotransmission, cellular transport, infection, and bacterial host defense. Among the RNA species, methylated nucleotides appear in most noncoding RNAs, constituting more than half of the post-transcriptional modifications identified so far. In particular, tRNA contains abundant methylated nucleotides, which stabilize the L-shaped tRNA structure and improve their molecular recognition (1-3).Among the methylated nucleotides in tRNA, N 2 ,N 2

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Crystal Structure of tRNA N2,N2-Guanosine Dimethyltransferase Trm1 from Pyrococcus horikoshii

Cited by 31 publications

References 50 publications

The tRNA Recognition Mechanism of Folate/FAD-dependent tRNA Methyltransferase (TrmFO)

The tRNA Recognition Mechanism of Folate/FAD-dependent tRNA Methyltransferase (TrmFO)

The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N²-methylguanosine at position 6 in tRNA

Substrate tRNA Recognition Mechanism of a Multisite-specific tRNA Methyltransferase, Aquifex aeolicus Trm1, Based on the X-ray Crystal Structure

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Crystal Structure of tRNA N2,N2-Guanosine Dimethyltransferase Trm1 from Pyrococcus horikoshii

Cited by 31 publications

References 50 publications

The tRNA Recognition Mechanism of Folate/FAD-dependent tRNA Methyltransferase (TrmFO)

The tRNA Recognition Mechanism of Folate/FAD-dependent tRNA Methyltransferase (TrmFO)

The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N2-methylguanosine at position 6 in tRNA

Substrate tRNA Recognition Mechanism of a Multisite-specific tRNA Methyltransferase, Aquifex aeolicus Trm1, Based on the X-ray Crystal Structure

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The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N²-methylguanosine at position 6 in tRNA