Solution structure of the ribosome recycling factor from Aquifex aeolicus.
The solution structure of ribosome recycling factor (RRF) from hyperthermophilic bacterium, Aquifex aeolicus, was determined by heteronuclear multidimensional NMR spectroscopy. Fifteen structures were calculated using restraints derived from NOE, J-coupling, and T1/T2 anisotropies. The resulting structure has an overall L-shaped conformation with two domains and is similar to that of a tRNA molecule. The domain I (corresponding to the anticodon stem of tRNA) is a rigid three alpha-helix bundle. Being slightly different from usual coiled-coil arrangements, each helix of domain I is not twisted but straight and parallel to the main axis. The domain II (corresponding to the portion with the CCA end of tRNA) is an alpha/beta domain with an alpha-helix and two beta-sheets, that has some flexible regions. The backbone atomic root-mean-square deviation (rmsd) values of both domains were 0.7 A when calculated separately, which is smaller than that of the molecule as a whole (1.4 A). Measurement of 15N-[1H] NOE values show that the residues in the corner of the L-shaped molecule are undergoing fast internal motion. These results indicate that the joint region between two domains contributes to the fluctuation in the orientation of two domains. Thus, it was shown that RRF remains the tRNA mimicry in solution where it functions.
Yoshida
T
T
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
Uchiyama
S
S
Nakano
H
H
Kashimori
H
H
Kijima
H
H
Ohshima
T
T
Saihara
Y
Y
Ishino
T
T
Shimahara
H
H
Yoshida
T
T
Yokose
K
K
Ohkubo
T
T
Kaji
A
A
Kobayashi
Y
Y
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000737:chemistry; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012269:Ribosomal Proteins; D012270:Ribosomes / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D012996:Solutions; D013816:Thermodynamics; D020124:Thermotoga maritima / Q000737:chemistry
D001426:Bacterial Proteins; D011506:Proteins; D012269:Ribosomal Proteins; D012996:Solutions; C087267:ribosome releasing factor