Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Science 11 March 1994:
Vol. 263. no. 5152, pp. 1404 - 1410
DOI: 10.1126/science.8128220
Prev | Table of Contents | Next

Articles

Science, Vol 263, Issue 5152, 1404-1410
Copyright © 1994 by American Association for the Advancement of Science

articles

The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser)

V Biou, A Yaremchuk, M Tukalo, and S Cusack

European Molecular Biology Laboratory, Grenoble Outstation, France.

The crystal structure of Thermus thermophilus seryl-transfer RNA synthetase, a class 2 aminoacyl-tRNA synthetase, complexed with a single tRNA(Ser) molecule was solved at 2.9 A resolution. The structure revealed how insertion of conserved base G20b from the D loop into the core of the tRNA determines the orientation of the long variable arm, which is a characteristic feature of most serine specific tRNAs. On tRNA binding, the antiparallel coiled-coil domain of one subunit of the synthetase makes contacts with the variable arm and T psi C loop of the tRNA and directs the acceptor stem of the tRNA into the active site of the other subunit. Specificity depends principally on recognition of the shape of tRNA(Ser) through backbone contacts and secondarily on sequence specific interactions.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Identification of Amino Acids in the N-terminal Domain of Atypical Methanogenic-type Seryl-tRNA Synthetase Critical for tRNA Recognition.
J. Jaric, S. Bilokapic, S. Lesjak, A. Crnkovic, N. Ban, and I. Weygand-Durasevic (2009)
J. Biol. Chem. 284, 30643-30651
   Abstract »    Full Text »    PDF »
Crystal structure of human selenocysteine tRNA.
Y. Itoh, S. Chiba, S.-i. Sekine, and S. Yokoyama (2009)
Nucleic Acids Res. 37, 6259-6268
   Abstract »    Full Text »    PDF »
The Human SepSecS-tRNASec Complex Reveals the Mechanism of Selenocysteine Formation.
S. Palioura, R. L. Sherrer, T. A. Steitz, D. Soll, and M. Simonovic (2009)
Science 325, 321-325
   Abstract »    Full Text »    PDF »
Unique protein architecture of alanyl-tRNA synthetase for aminoacylation, editing, and dimerization.
M. Naganuma, S.-i. Sekine, R. Fukunaga, and S. Yokoyama (2009)
PNAS 106, 8489-8494
   Abstract »    Full Text »    PDF »
Idiosyncratic Helix-Turn-Helix Motif in Methanosarcina barkeri Seryl-tRNA Synthetase Has a Critical Architectural Role.
S. Bilokapic, N. Ivic, V. Godinic-Mikulcic, I. Piantanida, N. Ban, and I. Weygand-Durasevic (2009)
J. Biol. Chem. 284, 10706-10713
   Abstract »    Full Text »    PDF »
Thermodynamic Analysis Reveals a Temperature-dependent Change in the Catalytic Mechanism of Bacillus stearothermophilus Tyrosyl-tRNA Synthetase.
G. Sharma and E. A. First (2009)
J. Biol. Chem. 284, 4179-4190
   Abstract »    Full Text »    PDF »
Analysis of genomic tRNA sets from Bacteria, Archaea, and Eukarya points to anticodon-codon hydrogen bonds as a major determinant of tRNA compositional variations.
I. Targanski and V. Cherkasova (2008)
RNA 14, 1095-1109
   Abstract »    Full Text »    PDF »
Evolution of acceptor stem tRNA recognition by class II prolyl-tRNA synthetase.
S. An, G. Barany, and K. Musier-Forsyth (2008)
Nucleic Acids Res. 36, 2514-2521
   Abstract »    Full Text »    PDF »
DNA mimicry by a high-affinity anti-NF-{kappa}B RNA aptamer.
N. J. Reiter, L. J. Maher III, and S. E. Butcher (2008)
Nucleic Acids Res. 36, 1227-1236
   Abstract »    Full Text »    PDF »
Predicting helical coaxial stacking in RNA multibranch loops.
R. Tyagi and D. H. Mathews (2007)
RNA 13, 939-951
   Abstract »    Full Text »    PDF »
Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA.
Y. Bessho, R. Shibata, S.-i. Sekine, K. Murayama, K. Higashijima, C. Hori-Takemoto, M. Shirouzu, S. Kuramitsu, and S. Yokoyama (2007)
PNAS 104, 8293-8298
   Abstract »    Full Text »    PDF »
Trypanosoma Seryl-tRNA Synthetase Is a Metazoan-like Enzyme with High Affinity for tRNASec.
R. Geslain, E. Aeby, T. Guitart, T. E. Jones, M. C. de Moura, F. Charriere, A. Schneider, and L. R. de Pouplana (2006)
J. Biol. Chem. 281, 38217-38225
   Abstract »    Full Text »    PDF »
Comprehensive Alanine-scanning Mutagenesis of Escherichia coli CsrA Defines Two Subdomains of Critical Functional Importance.
J. Mercante, K. Suzuki, X. Cheng, P. Babitzke, and T. Romeo (2006)
J. Biol. Chem. 281, 31832-31842
   Abstract »    Full Text »    PDF »
Biochemical Characterization of VlmL, a Seryl-tRNA Synthetase Encoded by the Valanimycin Biosynthetic Gene Cluster.
R. P. Garg, J. M. Gonzalez, and R. J. Parry (2006)
J. Biol. Chem. 281, 26785-26791
   Abstract »    Full Text »    PDF »
The Affinity of the Dynein Microtubule-binding Domain Is Modulated by the Conformation of Its Coiled-coil Stalk.
I. R. Gibbons, J. E. Garbarino, C. E. Tan, S. L. Reck-Peterson, R. D. Vale, and A. P. Carter (2005)
J. Biol. Chem. 280, 23960-23965
   Abstract »    Full Text »    PDF »
Differential Modes of Transfer RNASer Recognition in Methanosarcina barkeri.
D. Korencic, C. Polycarpo, I. Weygand-Durasevic, and D. Soll (2004)
J. Biol. Chem. 279, 48780-48786
   Abstract »    Full Text »    PDF »
Structure and Assembly of the RNA Binding Domain of Bluetongue Virus Non-structural Protein 2.
C. Butan, H. van der Zandt, and P. A. Tucker (2004)
J. Biol. Chem. 279, 37613-37621
   Abstract »    Full Text »    PDF »
Two distinct domains of the {beta} subunit of Aquifex aeolicus leucyl-tRNA synthetase are involved in tRNA binding as revealed by a three-hybrid selection.
Y.-G. Zheng, H. Wei, C. Ling, F. Martin, G. Eriani, and E.-D. Wang (2004)
Nucleic Acids Res. 32, 3294-3303
   Abstract »    Full Text »    PDF »
From The Cover: Automated protein crystal structure determination using ELVES.
J. Holton and T. Alber (2004)
PNAS 101, 1537-1542
   Abstract »    Full Text »    PDF »
Crystal Structure of the YchF Protein Reveals Binding Sites for GTP and Nucleic Acid.
A. Teplyakov, G. Obmolova, S. Y. Chu, J. Toedt, E. Eisenstein, A. J. Howard, and G. L. Gilliland (2003)
J. Bacteriol. 185, 4031-4037
   Abstract »    Full Text »    PDF »
Importance of the reverse Hoogsteen base pair 54-58 for tRNA function.
E. I. Zagryadskaya, F. R. Doyon, and S. V. Steinberg (2003)
Nucleic Acids Res. 31, 3946-3953
   Abstract »    Full Text »    PDF »
Functional Dissection of the Eukaryotic-specific tRNA-interacting Factor of Lysyl-tRNA Synthetase.
M. Francin and M. Mirande (2003)
J. Biol. Chem. 278, 1472-1479
   Abstract »    Full Text »    PDF »
NMR Analysis of Bovine tRNATrp. CONFORMATION DEPENDENCE OF Mg2+ BINDING.
Q. Gong, Q. Guo, K.-L. Tong, G. Zhu, J. T.-F. Wong, and H. Xue (2002)
J. Biol. Chem. 277, 20694-20701
   Abstract »    Full Text »    PDF »
Dual Mode Recognition of Two Isoacceptor tRNAs by Mammalian Mitochondrial Seryl-tRNA Synthetase.
N. Shimada, T. Suzuki, and K. Watanabe (2001)
J. Biol. Chem. 276, 46770-46778
   Abstract »    Full Text »    PDF »
Formation of Two Classes of tRNA Synthetases in Relation to Editing Functions and Genetic Code.
P. SCHIMMEL and L. RIBAS DE POUPLANA (2001)
Cold Spring Harb Symp Quant Biol 66, 161-166
   Abstract »    PDF »
RNA Determinants for Translational Editing. MISCHARGING A MINIHELIX SUBSTRATE BY A tRNA SYNTHETASE.
B. E. Nordin and P. Schimmel (1999)
J. Biol. Chem. 274, 6835-6838
   Abstract »    Full Text »    PDF »
Protection Patterns of tRNAs Do Not Change during Ribosomal Translocation.
M. Dabrowski, C. M. T. Spahn, M. A. Schafer, S. Patzke, and K. H. Nierhaus (1998)
J. Biol. Chem. 273, 32793-32800
   Abstract »    Full Text »    PDF »
Redesigning Enzyme Topology by Directed Evolution.
G. MacBeath, P. Kast, and D. Hilvert (1998)
Science 279, 1958-1961
   Abstract »    Full Text »
The importance of tRNA backbone-mediated interactions with synthetase for aminoacylation.
W. H. McClain, J. Schneider, S. Bhattacharya, and K. Gabriel (1998)
PNAS 95, 460-465
   Abstract »    Full Text »    PDF »
Detection of Noncovalent tRNA·Aminoacyl-tRNA Synthetase Complexes by Matrix-assisted Laser Desorption/Ionization Mass Spectrometry.
I. Gruic-Sovulj, H.-C. Ludemann, F. Hillenkamp, I. Weygand-Durasevic, Z. Kucan, and J. Peter-Katalinic (1997)
J. Biol. Chem. 272, 32084-32091
   Abstract »    Full Text »    PDF »
Mapping the Inside of the Ribosome with an RNA Helical Ruler.
S. Joseph, B. Weiser, and H. F. Noller (1997)
Science 278, 1093-1098
   Abstract »    Full Text »
Molding a peptide into an RNA site by in vivo peptide evolution.
K. Harada, S. S. Martin, R. Tan, and A. D. Frankel (1997)
PNAS 94, 11887-11892
   Abstract »    Full Text »    PDF »
Domain Structure of Thermus thermophilus UvrB Protein. SIMILARITY IN DOMAIN STRUCTURE TO A HELICASE.
N. Nakagawa, R. Masui, R. Kato, and S. Kuramitsu (1997)
J. Biol. Chem. 272, 22703-22713
   Abstract »    Full Text »    PDF »
alpha -Helical Protein Assembly Motifs.
W. D. Kohn, C. T. Mant, and R. S. Hodges (1997)
J. Biol. Chem. 272, 2583-2586
   Full Text »    PDF »
Defining the Active Site of Yeast Seryl-tRNA Synthetase. MUTATIONS IN MOTIF 2LOOP RESIDUES AFFECT tRNA-DEPENDENT AMINO ACID RECOGNITION.
B. Lenhard, B. Lenhard, I. Landeka, and D. Soll (1997)
J. Biol. Chem. 272, 1136-1141
   Abstract »    Full Text »    PDF »
Length suppression in histone messenger RNA 3'-end maturation: Processing defects of insertion mutant premessenger RNAs can be compensated by insertions into the U7 small nuclear RNA.
E. C. Scharl and J. A. Steitz (1996)
PNAS 93, 14659-14664
   Abstract »    Full Text »    PDF »
Expression of Rat Aspartyl-tRNA Synthetase in Saccharomyces cerevisiae. ROLE OF THE NH2-TERMINAL POLYPEPTIDE EXTENSION ON ENZYME ACTIVITY AND STABILITY.
F. Agou, J.-P. Waller, and M. Mirande (1996)
J. Biol. Chem. 271, 29295-29303
   Abstract »    Full Text »    PDF »
The C-terminal Extension of Yeast Seryl-tRNA Synthetase Affects Stability of the Enzyme and Its Substrate Affinity.
I. Weygand-Durasevic, B. Lenhard, S. Filipic, and D. Söll (1996)
J. Biol. Chem. 271, 2455-2461
   Abstract »    Full Text »    PDF »
Essential Amino Acids Regulate Fatty Acid Synthase Expression through an Uncharged Transfer RNA-dependent Mechanism.
S. M. Dudek and C. F. Semenkovich (1995)
J. Biol. Chem. 270, 29323-29329
   Abstract »    Full Text »    PDF »
Altering specific telomerase RNA template residues affects active site function..
D Gilley, M S Lee, and E H Blackburn (1995)
Genes & Dev. 9, 2214-2226
   Abstract »    PDF »
Selenocysteylation in Eukaryotes Necessitates the Uniquely Long Aminoacyl Acceptor Stem of Selenocysteine tRNA[IMAGE].
C. Sturchler-Pierrat, N. Hubert, T. Totsuka, T. Mizutani, P. Carbon, and A. Krol (1995)
J. Biol. Chem. 270, 18570-18574
   Abstract »    Full Text »    PDF »
Crystal structure of the T4 regA translational regulator protein at 1.9 A resolution.
C Kang, R Chan, I Berger, C Lockshin, L Green, L Gold, and A Rich (1995)
Science 268, 1170-1173
   Abstract »    PDF »
Architectures of class-defining and specific domains of glutamyl-tRNA synthetase.
O Nureki, D. Vassylyev, K Katayanagi, T Shimizu, S Sekine, T Kigawa, T Miyazawa, S Yokoyama, and K Morikawa (1995)
Science 267, 1958-1965
   Abstract »    PDF »
Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate.
H Belrhali, A Yaremchuk, M Tukalo, K Larsen, C Berthet-Colominas, R Leberman, B Beijer, B Sproat, J Als-Nielsen, G Grubel, et al. (1994)
Science 263, 1432-1436
   Abstract »    PDF »
Equilibrium Unfolding of Bombyx mori Glycyl-tRNA Synthetase.
J. D. Dignam, X. Qu, and J. B. Chaires (2001)
J. Biol. Chem. 276, 4028-4037
   Abstract »    Full Text »    PDF »
Importance of the Anticodon Sequence in the Aminoacylation of tRNAs by Methionyl-tRNA Synthetase and by Valyl-tRNA Synthetase in an Archaebacterium.
V. Ramesh and U. L. RajBhandary (2001)
J. Biol. Chem. 276, 3660-3665
   Abstract »    Full Text »    PDF »
Characterization and tRNA Recognition of Mammalian Mitochondrial Seryl-tRNA Synthetase.
T. Yokogawa, N. Shimada, N. Takeuchi, L. Benkowski, T. Suzuki, A. Omori, T. Ueda, K. Nishikawa, L. L. Spremulli, and K. Watanabe (2000)
J. Biol. Chem. 275, 19913-19920
   Abstract »    Full Text »    PDF »
From the Cover: Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase.
A. Shimada, O. Nureki, M. Goto, S. Takahashi, and S. Yokoyama (2001)
PNAS 98, 13537-13542
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)