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Crystal structure of tRNA m(1)A58 methyltransferase TrmI from Aquifex aeolicus in complex with S-adenosyl-L-methionine.

Kuratani M, Yanagisawa T, Ishii R, Matsuno M, Si SY, Katsura K, Ushikoshi-Nakayama R, Shibata R, Shirouzu M, Bessho Y, Yokoyama S - J. Struct. Funct. Genomics (2014)

Bottom Line: The N (1)-methyladenosine residue at position 58 of tRNA is found in the three domains of life, and contributes to the stability of the three-dimensional L-shaped tRNA structure.Based on a comparison of the AdoMet binding mode of A. aeolicus TrmI to those of the Thermus thermophilus and Pyrococcus abyssi TrmIs, we discuss their similarities and differences.Although the binding modes to the N6 amino group of the adenine moiety of AdoMet are similar, using the side chains of acidic residues as well as hydrogen bonds, the positions of the amino acid residues involved in binding are diverse among the TrmIs from A. aeolicus, T. thermophilus, and P. abyssi.

View Article: PubMed Central - PubMed

Affiliation: RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.

ABSTRACT
The N (1)-methyladenosine residue at position 58 of tRNA is found in the three domains of life, and contributes to the stability of the three-dimensional L-shaped tRNA structure. In thermophilic bacteria, this modification is important for thermal adaptation, and is catalyzed by the tRNA m(1)A58 methyltransferase TrmI, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. We present the 2.2 Å crystal structure of TrmI from the extremely thermophilic bacterium Aquifex aeolicus, in complex with AdoMet. There are four molecules per asymmetric unit, and they form a tetramer. Based on a comparison of the AdoMet binding mode of A. aeolicus TrmI to those of the Thermus thermophilus and Pyrococcus abyssi TrmIs, we discuss their similarities and differences. Although the binding modes to the N6 amino group of the adenine moiety of AdoMet are similar, using the side chains of acidic residues as well as hydrogen bonds, the positions of the amino acid residues involved in binding are diverse among the TrmIs from A. aeolicus, T. thermophilus, and P. abyssi.

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Crystal structure of A. aeolicus TrmI in complex with AdoMet. a The tetrameric structure of A. aeolicus TrmI. The four protomers are colored pink, cyan, purple, and green. b Protomer structure of A. aeolicus TrmI. The N-terminal domain, the linker helix, and the C-terminal domain are colored pink, purple, and cyan, respectively. The secondary structures are labeled. c The calculated distributions c(M) by Sedfit [30]. d–fBall-and-stick representations of AdoMet binding by A. aeolicus TrmI (chain A) (d), T. thermophilus TrmI [19] (chain A) (e), and P. abyssi TrmI [20] (chain A) (f). The three amino acid residues surrounding the N6 amino group of AdoMet are labeled with orange rectangles. Hydrogen bonds are depicted by dotted lines with their distances (Å). The figures were created using CueMol (http://cuemol.sourceforge.jp/en/)
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Fig1: Crystal structure of A. aeolicus TrmI in complex with AdoMet. a The tetrameric structure of A. aeolicus TrmI. The four protomers are colored pink, cyan, purple, and green. b Protomer structure of A. aeolicus TrmI. The N-terminal domain, the linker helix, and the C-terminal domain are colored pink, purple, and cyan, respectively. The secondary structures are labeled. c The calculated distributions c(M) by Sedfit [30]. d–fBall-and-stick representations of AdoMet binding by A. aeolicus TrmI (chain A) (d), T. thermophilus TrmI [19] (chain A) (e), and P. abyssi TrmI [20] (chain A) (f). The three amino acid residues surrounding the N6 amino group of AdoMet are labeled with orange rectangles. Hydrogen bonds are depicted by dotted lines with their distances (Å). The figures were created using CueMol (http://cuemol.sourceforge.jp/en/)

Mentions: The crystal structure of A. aeolicus TrmI was determined at 2.2 Å resolution by the molecular replacement method, and was refined to Rwork and Rfree factors of 19.6 and 23.0 %, respectively (Table 1). The asymmetric unit contains four protomers (A–D) (Fig. 1a) and four AdoMet molecules. The electron density was interpretable for 247 residues (Asn2–Thr248). The A. aeolicus TrmI protomer (Fig. 1b) consists of the small N-terminal domain (residues 2–58) and the C-terminal methyltransferase domain (residues 72–248), which are connected by an α-helical linker (residues 59–71). The N-terminal domain forms a small β sandwich (Fig. 1b), in which the β sheet β2–β1–β6–β5 stacks on the β hairpin β3–β4, along with the small 310-helix η1. The C-terminal domain adopts the typical type I methyltransferase fold, with a central seven-stranded β sheet with the topology β9–β8–β7–β10–β11–β14–β12, flanked by α helices on both sides (Fig. 1b). As reported previously [19], the long β strand β12, in which the head interacts with β13, is characteristic of TrmI among the type I methyltransferases, and it provides a surface for tetramerization.Fig. 1


Crystal structure of tRNA m(1)A58 methyltransferase TrmI from Aquifex aeolicus in complex with S-adenosyl-L-methionine.

Kuratani M, Yanagisawa T, Ishii R, Matsuno M, Si SY, Katsura K, Ushikoshi-Nakayama R, Shibata R, Shirouzu M, Bessho Y, Yokoyama S - J. Struct. Funct. Genomics (2014)

Crystal structure of A. aeolicus TrmI in complex with AdoMet. a The tetrameric structure of A. aeolicus TrmI. The four protomers are colored pink, cyan, purple, and green. b Protomer structure of A. aeolicus TrmI. The N-terminal domain, the linker helix, and the C-terminal domain are colored pink, purple, and cyan, respectively. The secondary structures are labeled. c The calculated distributions c(M) by Sedfit [30]. d–fBall-and-stick representations of AdoMet binding by A. aeolicus TrmI (chain A) (d), T. thermophilus TrmI [19] (chain A) (e), and P. abyssi TrmI [20] (chain A) (f). The three amino acid residues surrounding the N6 amino group of AdoMet are labeled with orange rectangles. Hydrogen bonds are depicted by dotted lines with their distances (Å). The figures were created using CueMol (http://cuemol.sourceforge.jp/en/)
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Related In: Results  -  Collection

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Fig1: Crystal structure of A. aeolicus TrmI in complex with AdoMet. a The tetrameric structure of A. aeolicus TrmI. The four protomers are colored pink, cyan, purple, and green. b Protomer structure of A. aeolicus TrmI. The N-terminal domain, the linker helix, and the C-terminal domain are colored pink, purple, and cyan, respectively. The secondary structures are labeled. c The calculated distributions c(M) by Sedfit [30]. d–fBall-and-stick representations of AdoMet binding by A. aeolicus TrmI (chain A) (d), T. thermophilus TrmI [19] (chain A) (e), and P. abyssi TrmI [20] (chain A) (f). The three amino acid residues surrounding the N6 amino group of AdoMet are labeled with orange rectangles. Hydrogen bonds are depicted by dotted lines with their distances (Å). The figures were created using CueMol (http://cuemol.sourceforge.jp/en/)
Mentions: The crystal structure of A. aeolicus TrmI was determined at 2.2 Å resolution by the molecular replacement method, and was refined to Rwork and Rfree factors of 19.6 and 23.0 %, respectively (Table 1). The asymmetric unit contains four protomers (A–D) (Fig. 1a) and four AdoMet molecules. The electron density was interpretable for 247 residues (Asn2–Thr248). The A. aeolicus TrmI protomer (Fig. 1b) consists of the small N-terminal domain (residues 2–58) and the C-terminal methyltransferase domain (residues 72–248), which are connected by an α-helical linker (residues 59–71). The N-terminal domain forms a small β sandwich (Fig. 1b), in which the β sheet β2–β1–β6–β5 stacks on the β hairpin β3–β4, along with the small 310-helix η1. The C-terminal domain adopts the typical type I methyltransferase fold, with a central seven-stranded β sheet with the topology β9–β8–β7–β10–β11–β14–β12, flanked by α helices on both sides (Fig. 1b). As reported previously [19], the long β strand β12, in which the head interacts with β13, is characteristic of TrmI among the type I methyltransferases, and it provides a surface for tetramerization.Fig. 1

Bottom Line: The N (1)-methyladenosine residue at position 58 of tRNA is found in the three domains of life, and contributes to the stability of the three-dimensional L-shaped tRNA structure.Based on a comparison of the AdoMet binding mode of A. aeolicus TrmI to those of the Thermus thermophilus and Pyrococcus abyssi TrmIs, we discuss their similarities and differences.Although the binding modes to the N6 amino group of the adenine moiety of AdoMet are similar, using the side chains of acidic residues as well as hydrogen bonds, the positions of the amino acid residues involved in binding are diverse among the TrmIs from A. aeolicus, T. thermophilus, and P. abyssi.

View Article: PubMed Central - PubMed

Affiliation: RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.

ABSTRACT
The N (1)-methyladenosine residue at position 58 of tRNA is found in the three domains of life, and contributes to the stability of the three-dimensional L-shaped tRNA structure. In thermophilic bacteria, this modification is important for thermal adaptation, and is catalyzed by the tRNA m(1)A58 methyltransferase TrmI, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. We present the 2.2 Å crystal structure of TrmI from the extremely thermophilic bacterium Aquifex aeolicus, in complex with AdoMet. There are four molecules per asymmetric unit, and they form a tetramer. Based on a comparison of the AdoMet binding mode of A. aeolicus TrmI to those of the Thermus thermophilus and Pyrococcus abyssi TrmIs, we discuss their similarities and differences. Although the binding modes to the N6 amino group of the adenine moiety of AdoMet are similar, using the side chains of acidic residues as well as hydrogen bonds, the positions of the amino acid residues involved in binding are diverse among the TrmIs from A. aeolicus, T. thermophilus, and P. abyssi.

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