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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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Sequence alignment of TrmI proteins. The amino acid sequences of A. aeolicus TrmI (AaTrmI), T. maritima TrmI (TmTrmI), T. thermophilus TrmI (TtTrmI), M. tuberculosis TrmI (MtTrmI), P. abyssi TrmI (PaTrmI), and H. sapiens Trm61 (HsTrm61) were aligned with ClustalX 2.1 [31]. Identical residues are white in a red background. Similar residues are red in blue rectangles. The secondary structures of A. aeolicus TrmI (PDB: 2YVL) and H. sapiens Trm61 (PDB: 2B25) are shown at the top and bottom, respectively. The three amino acid residues with side chains located near the N6 amino group of AdoMet are indicated by orange triangles. The figure was depicted by ESPript [32]
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Fig2: Sequence alignment of TrmI proteins. The amino acid sequences of A. aeolicus TrmI (AaTrmI), T. maritima TrmI (TmTrmI), T. thermophilus TrmI (TtTrmI), M. tuberculosis TrmI (MtTrmI), P. abyssi TrmI (PaTrmI), and H. sapiens Trm61 (HsTrm61) were aligned with ClustalX 2.1 [31]. Identical residues are white in a red background. Similar residues are red in blue rectangles. The secondary structures of A. aeolicus TrmI (PDB: 2YVL) and H. sapiens Trm61 (PDB: 2B25) are shown at the top and bottom, respectively. The three amino acid residues with side chains located near the N6 amino group of AdoMet are indicated by orange triangles. The figure was depicted by ESPript [32]

Mentions: We compared the structure of A. aeolicus TrmI to those of T. thermophilus TrmI in complex with S-adenosyl-l-homocysteine (AdoHcy) (Fig. 1e) and P. abyssi TrmI in complex with AdoMet (Fig. 1f), and examined the conservation of residues involved in AdoMet binding. A. aeolicus, T. thermophilus, and P. abyssi all live in high-temperature environments. The N6 amino group of the adenine moiety is recognized in diverse manners by the various TrmI structures. The side chains of three amino acid residues (Asp148, Lys150, and Tyr172 in A. aeolicus TrmI; Fig. 2) surround the N6 amino group, and the underlined residues are involved in AdoMet binding. In the corresponding three positions, T. thermophilus TrmI has Lys153, Glu155, and Val177, while P. abyssi TrmI has Asp153, Tyr155, and Val176 (Fig. 2). Asp148 and Tyr172 of A. aeolicus TrmI form direct hydrogen bonds with the N6 amino group (Fig. 1d). In T. thermophilus TrmI (Fig. 1e) [19], the side chain of Glu155 and a water molecule form hydrogen bonds with the N6 amino group, and these are apparently equivalent to the two hydrogen bonds formed between this moiety and A. aeolicus TrmI. However, Glu155 of T. thermophilus TrmI is located at a different position than Asp148 of A. aeolicus TrmI in the amino acid alignment (Fig. 2). On the other hand, P. abyssi TrmI forms only one hydrogen bond by Asp153 (Fig. 1f) [20], which is located at the same position as Asp148 of A. aeolicus TrmI (Fig. 2). The distances from the N6 amino group to the three water molecules (Fig. 1f) are 3.8, 3.9, and 5.5 Å, respectively. The N7 atom of AdoMet is bound to TrmI by one water-mediated hydrogen bond, although the side chains involved in its coordination differ (Fig. 1d–f).Fig. 2


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)

Sequence alignment of TrmI proteins. The amino acid sequences of A. aeolicus TrmI (AaTrmI), T. maritima TrmI (TmTrmI), T. thermophilus TrmI (TtTrmI), M. tuberculosis TrmI (MtTrmI), P. abyssi TrmI (PaTrmI), and H. sapiens Trm61 (HsTrm61) were aligned with ClustalX 2.1 [31]. Identical residues are white in a red background. Similar residues are red in blue rectangles. The secondary structures of A. aeolicus TrmI (PDB: 2YVL) and H. sapiens Trm61 (PDB: 2B25) are shown at the top and bottom, respectively. The three amino acid residues with side chains located near the N6 amino group of AdoMet are indicated by orange triangles. The figure was depicted by ESPript [32]
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Related In: Results  -  Collection

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Fig2: Sequence alignment of TrmI proteins. The amino acid sequences of A. aeolicus TrmI (AaTrmI), T. maritima TrmI (TmTrmI), T. thermophilus TrmI (TtTrmI), M. tuberculosis TrmI (MtTrmI), P. abyssi TrmI (PaTrmI), and H. sapiens Trm61 (HsTrm61) were aligned with ClustalX 2.1 [31]. Identical residues are white in a red background. Similar residues are red in blue rectangles. The secondary structures of A. aeolicus TrmI (PDB: 2YVL) and H. sapiens Trm61 (PDB: 2B25) are shown at the top and bottom, respectively. The three amino acid residues with side chains located near the N6 amino group of AdoMet are indicated by orange triangles. The figure was depicted by ESPript [32]
Mentions: We compared the structure of A. aeolicus TrmI to those of T. thermophilus TrmI in complex with S-adenosyl-l-homocysteine (AdoHcy) (Fig. 1e) and P. abyssi TrmI in complex with AdoMet (Fig. 1f), and examined the conservation of residues involved in AdoMet binding. A. aeolicus, T. thermophilus, and P. abyssi all live in high-temperature environments. The N6 amino group of the adenine moiety is recognized in diverse manners by the various TrmI structures. The side chains of three amino acid residues (Asp148, Lys150, and Tyr172 in A. aeolicus TrmI; Fig. 2) surround the N6 amino group, and the underlined residues are involved in AdoMet binding. In the corresponding three positions, T. thermophilus TrmI has Lys153, Glu155, and Val177, while P. abyssi TrmI has Asp153, Tyr155, and Val176 (Fig. 2). Asp148 and Tyr172 of A. aeolicus TrmI form direct hydrogen bonds with the N6 amino group (Fig. 1d). In T. thermophilus TrmI (Fig. 1e) [19], the side chain of Glu155 and a water molecule form hydrogen bonds with the N6 amino group, and these are apparently equivalent to the two hydrogen bonds formed between this moiety and A. aeolicus TrmI. However, Glu155 of T. thermophilus TrmI is located at a different position than Asp148 of A. aeolicus TrmI in the amino acid alignment (Fig. 2). On the other hand, P. abyssi TrmI forms only one hydrogen bond by Asp153 (Fig. 1f) [20], which is located at the same position as Asp148 of A. aeolicus TrmI (Fig. 2). The distances from the N6 amino group to the three water molecules (Fig. 1f) are 3.8, 3.9, and 5.5 Å, respectively. The N7 atom of AdoMet is bound to TrmI by one water-mediated hydrogen bond, although the side chains involved in its coordination differ (Fig. 1d–f).Fig. 2

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.

Show MeSH
Related in: MedlinePlus