TY - JOUR
T1 - Deep knot structure for construction of active site and cofactor binding site of tRNA modification enzyme
AU - Nureki, Osamu
AU - Watanabe, Kazunori
AU - Fukai, Shuya
AU - Ishii, Ryohei
AU - Endo, Yaeta
AU - Hori, Hiroyuki
AU - Yokoyama, Shigeyuki
N1 - Funding Information:
This work was supported by a PRESTO Program grant from JST (Japan Science and Technology) to O.N., a Naito Foundation grant to O.N., and by Grants-in-Aid for Science Research on Priority Areas (15032209) to O.N. and Grants-in-Aid for Science Research (13680692) to H.H., from the Ministry of Education, Culture, Sports, Science, and Technology of Japan. This work was also supported by the RIKEN Structural Genomics/Proteomics Initiative (RSGI), the National Project on Protein Structural and Functional Analyses, Ministry of Education, Culture, Sports, Science, and Technology of Japan. We are greatly indebted to Drs. M. Kawamoto and H. Sakai (JASRI) for their help in data collection at SPring-8.
PY - 2004/4
Y1 - 2004/4
N2 - 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.
AB - 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.
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U2 - 10.1016/j.str.2004.03.003
DO - 10.1016/j.str.2004.03.003
M3 - Article
C2 - 15062082
AN - SCOPUS:1842607227
VL - 12
SP - 593
EP - 602
JO - Structure with Folding & design
JF - Structure with Folding & design
SN - 0969-2126
IS - 4
ER -