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 journalArticle

90 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 languageEnglish
Pages (from-to)593-602
Number of pages10
JournalStructure
Volume12
Issue number4
DOIs
Publication statusPublished - Apr 2004
Externally publishedYes

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

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 journalArticle

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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AU - Hori, Hiroyuki

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