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Journal of Biochemistry Advance Access published online on July 26, 2006
Journal of Biochemistry, doi:10.1093/jb/mvj164
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© 2006 The Japanese Biochemical Society.
Received May 1, 2006
Accepted July 11, 2006

Regular Paper

Crystal Structures of the Nicotiana glutinosa Ribonuclease NT in Complex with Nucleoside Monophosphates

Shin Kawano 1, Yoshimitsu Kakuta 1, Takashi Nakashima 1, and Makoto Kimura 1 *

1 Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka 812-8581, Japan

* To whom correspondence should be addressed.
Makoto Kimura, E-mail: mkimura{at}agr.kyushu-u.ac.jp


  Abstract

Ribonuclease NT (RNase NT), induced upon tobacco mosaic virus (TMV) infection in Nicotiana glutinosa leaves, has a broad base specificity. The crystal structures of RNase NT in complex with either 5'-AMP, 5'-GMP, or 2'-UMP were determined at 1.8 Å resolutions by molecular replacement. RNase NT consists of seven helices and seven {beta} strands, and the structure is highly similar to that of RNase NW, a guanylic acid preferential RNase from the N. glutinosa leaves, showing root mean square deviation (rmsd) of 1.1 Å over an entire length of two molecules for C{alpha} atoms. The complex structures revealed that Trp42, Asn44, and Trp50 are involved in interactions with bases at B1 site (primary site), whereas Gln12, Tyr17, Ser78, Leu79, and Phe89 participate in recognition of bases at B2 site (subsite). The 5'-GMP and 5'-AMP bind both B1 and B2 sites in RNase NT, while 2'-UMP predominantly binds B1 site in the complex. The nucleotide binding modes in these complexes would provide a clue to elucidation of structural basis for the broad base specificity for RNase NT.

Keywords: crystal structure; Nicotiana glutinosa; base specificity; nucleotide binding; RNase.
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