Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme

Osamu Nureki; Kazunori Watanabe; Shuya Fukai; Ryohei Ishii; Yaeta Endo; Hiroyuki Hori; Shigeyuki Yokoyama

doi:10.1016/j.str.2004.03.003

Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme

Osamu Nureki, Kazunori Watanabe, Shuya Fukai, Ryohei Ishii, Yaeta Endo, Hiroyuki Hori, Shigeyuki Yokoyama

Research output: Contribution to journal › Article

91 Citations (Scopus)

Abstract

The tRNA(Gm18) methyltransferase (TrmH) catalyzes the 2′-O methylation of guanosine 18 (Gua18) of tRNA. We solved the crystal structure of Thermus thermophilus TrmH complexed with S-adenosyl-L-methionine at 1.85 Å resolution. The catalytic domain contains a deep trefoil knot, which mutational analyses revealed to be crucial for the formation of the catalytic site and the cofactor binding pocket. The tRNA dihydrouridine(D)-arm can be docked onto the dimeric TrmH, so that the tRNA D-stem is clamped by the N- and C-terminal helices from one subunit while the Gua18 is modified by the other subunit. Arg41 from the other subunit enters the catalytic site and forms a hydrogen bond with a bound sulfate ion, an RNA main chain phosphate analog, thus activating its nucleophilic state. Based on Gua18 modeling onto the active site, we propose that once Gua18 binds, the phosphate group activates Arg41, which then deprotonates the 2′-OH group for methylation.

Original language	English
Pages (from-to)	593-602
Number of pages	10
Journal	Structure
Volume	12
Issue number	4
DOIs	https://doi.org/10.1016/j.str.2004.03.003
Publication status	Published - Apr 2004
Externally published	Yes

Fingerprint

Guanosine

Transfer RNA

Catalytic Domain

Binding Sites

Enzymes

Methylation

tRNA Methyltransferases

Phosphates

Thermus thermophilus

S-Adenosylmethionine

Sulfates

Hydrogen

RNA

Ions

ASJC Scopus subject areas

Molecular Biology
Structural Biology

Cite this

Nureki, O., Watanabe, K., Fukai, S., Ishii, R., Endo, Y., Hori, H., & Yokoyama, S. (2004). Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure, 12(4), 593-602. https://doi.org/10.1016/j.str.2004.03.003

Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. / Nureki, Osamu; Watanabe, Kazunori; Fukai, Shuya; Ishii, Ryohei; Endo, Yaeta; Hori, Hiroyuki; Yokoyama, Shigeyuki.

In: Structure, Vol. 12, No. 4, 04.2004, p. 593-602.

Research output: Contribution to journal › Article

Nureki, O, Watanabe, K, Fukai, S, Ishii, R, Endo, Y, Hori, H & Yokoyama, S 2004, 'Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme', Structure, vol. 12, no. 4, pp. 593-602. https://doi.org/10.1016/j.str.2004.03.003

Nureki O, Watanabe K, Fukai S, Ishii R, Endo Y, Hori H et al. Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. Structure. 2004 Apr;12(4):593-602. https://doi.org/10.1016/j.str.2004.03.003

Nureki, Osamu ; Watanabe, Kazunori ; Fukai, Shuya ; Ishii, Ryohei ; Endo, Yaeta ; Hori, Hiroyuki ; Yokoyama, Shigeyuki. / Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme. In: Structure. 2004 ; Vol. 12, No. 4. pp. 593-602.

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10.1016/j.str.2004.03.003