Shape-selective RNA recognition by cysteinyl-tRNA synthetase

The crystal structure of Escherichia coli cysteinyl-tRNA synthetase (CysRS) bound to tRNACys at a resolution of 2.3 Å reveals base-specific and shape-selective interactions across an extensive protein-RNA recognition interface. The complex contains a mixed α/β C-terminal domain, which is disordered in the unliganded enzyme. This domain makes specific hydrogen bonding interactions with all three bases of the GCA anticodon. The tRNA anticodon stem is bent sharply toward the enzyme as compared with its conformation when bound to elongation factor Tu, providing an essential basis for shape-selective recognition. The CysRS structure also reveals interactions of conserved enzyme groups with the sugar-phosphate backbone in the D loop, adjacent to an unusual G15·G48 tertiary base pair previously implicated in tRNA aminoacylation. A combined mutational analysis of enzyme and tRNA groups at G15·G48 supports the notion that contacts between CysRS and the sugar-phosphate backbone contribute to recognition by indirect readout.

[1]  G. Eriani,et al.  L‐Arginine recognition by yeast arginyl‐tRNA synthetase , 1998, The EMBO journal.

[2]  T. Steitz,et al.  Structural basis for misaminoacylation by mutant E. coli glutaminyl-tRNA synthetase enzymes. , 1989, Science.

[3]  B. Connolly,et al.  Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[4]  J. Perona,et al.  Crystallization and preliminary diffraction analysis of Escherichia coli cysteinyl-tRNA synthetase. , 1999, Acta crystallographica. Section D, Biological crystallography.

[5]  J. Dunn,et al.  ompT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification , 1988, Journal of bacteriology.

[6]  J. Perona,et al.  Amino acid discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants. , 2003, Journal of molecular biology.

[7]  L. Pallanck,et al.  The anticodon and discriminator base are major determinants of cysteine tRNA identity in vivo. , 1992, The Journal of biological chemistry.

[8]  Duncan E McRee,et al.  Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Shigeyuki Yokoyama,et al.  Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase. , 2003, RNA.

[10]  K. Wilson,et al.  The name is bond — H bond , 1999, Nature Structural Biology.

[11]  Phoebe A Rice,et al.  Integration host factor: putting a twist on protein-DNA recognition. , 2003, Journal of molecular biology.

[12]  Shigeyuki Yokoyama,et al.  ATP binding by glutamyl‐tRNA synthetase is switched to the productive mode by tRNA binding , 2003, The EMBO journal.

[13]  O. Nureki,et al.  Structural Basis for the Recognition of Isoleucyl-Adenylate and an Antibiotic, Mupirocin, by Isoleucyl-tRNA Synthetase* , 2001, The Journal of Biological Chemistry.

[14]  N. Seeman,et al.  Sequence-specific Recognition of Double Helical Nucleic Acids by Proteins (base Pairs/hydrogen Bonding/recognition Fidelity/ion Binding) , 2022 .

[15]  B. Chernov,et al.  SITE-SPECIFIC MUTAGENESIS OF THE LYS-172 RESIDUE IN PHAGE T7 RNA POLYMERASE : CHARACTERIZATION OF THE TRANSCRIPTIONAL PROPERTIES OF MUTANT PROTEINS , 1992 .

[16]  Y. Hou,et al.  Probing a tRNA core that contributes to aminoacylation. , 2000, Journal of molecular biology.

[17]  A. Fersht,et al.  Active site titration and aminoacyl adenylate binding stoichiometry of aminoacyl-tRNA synthetases. , 1975, Biochemistry.

[18]  T. Steitz,et al.  Insights into editing from an ile-tRNA synthetase structure with tRNAile and mupirocin. , 1999 .

[19]  Ya-Ming Hou,et al.  Enzymatic aminoacylation of tRNA acceptor stem helices with cysteine is dependent on a single nucleotide. , 1995, Biochemistry.

[20]  J. Williamson.  Induced fit in RNA–protein recognition , 2000, Nature Structural Biology.

[21]  O. Nureki,et al.  Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[22]  Kristina M Smith,et al.  Recognition of tRNA backbone for aminoacylation with cysteine: evolution from Escherichia coli to human. , 2002, Journal of molecular biology.

[23]  A. Fersht,et al.  Cysteinyl-tRNA synthetase from Escherichia coli does not need an editing mechanism to reject serine and alanine. High binding energy of small groups in specific molecular interactions. , 1979, Biochemistry.

[24]  D. Turner,et al.  Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs. , 1999, Journal of molecular biology.

[25]  O. Uhlenbeck,et al.  Chemical and enzymatic synthesis of tRNAs for high-throughput crystallization. , 2001, RNA.

[26]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[27]  Shigeyuki Yokoyama,et al.  Structural Basis for Double-Sieve Discrimination of L-Valine from L-Isoleucine and L-Threonine by the Complex of tRNAVal and Valyl-tRNA Synthetase , 2000, Cell.

[28]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[29]  P. Schimmel,et al.  Sequence determination and modeling of structural motifs for the smallest monomeric aminoacyl-tRNA synthetase. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[30]  J. Perona,et al.  Structural origins of amino acid selection without editing by cysteinyl‐tRNA synthetase , 2002, The EMBO journal.

[31]  John J. Perona,et al.  Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease , 1998, Nature Structural Biology.

[32]  R Giegé,et al.  Universal rules and idiosyncratic features in tRNA identity. , 1998, Nucleic acids research.

[33]  C. Evilia,et al.  Alternative design of a tRNA core for aminoacylation. , 2000, Journal of molecular biology.

[34]  J. Schwabe,et al.  Towards an understanding of protein-DNA recognition. , 1996, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[35]  M. Levitt.  Detailed Molecular Model for Transfer Ribonucleic Acid , 1969, Nature.

[36]  O. Nureki,et al.  Major identity determinants in the "augmented D helix" of tRNA(Glu) from Escherichia coli. , 1996, Journal of molecular biology.

[37]  J. Perona,et al.  Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases. , 2000, Journal of molecular biology.

[38]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[39]  J. Perona,et al.  Zinc-mediated amino acid discrimination in cysteinyl-tRNA synthetase. , 2003, Journal of molecular biology.

[40]  D. E. Ruffner,et al.  Modified crush-and-soak method for recovering oligodeoxynucleotides from polyacrylamide gel. , 1996, BioTechniques.

[41]  A. Joachimiak,et al.  Crystal structure of trp represser/operator complex at atomic resolution , 1988, Nature.

[42]  P. Brick,et al.  Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. , 1989, Journal of molecular biology.

[43]  S Cusack,et al.  The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). , 1994, Science.

[44]  Samuel Selvaraj,et al.  Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. , 2004, Journal of molecular biology.

[45]  D. Söll,et al.  Aminoacyl-tRNA synthesis. , 2000, Annual review of biochemistry.

[46]  G. Eriani,et al.  Cysteinyl-tRNA synthetase: determination of the last E. coli aminoacyl-tRNA synthetase primary structure. , 1991, Nucleic acids research.

[47]  Ya-Ming Hou,et al.  Aminoacylation of tRNA in the evolution of an aminoacyl-tRNA synthetase. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[48]  Y. Hou.  Structural elements that contribute to an unusual tertiary interaction in a transfer RNA. , 1994, Biochemistry.

[49]  Dino Moras,et al.  tRNA aminoacylation by arginyl‐tRNA synthetase: induced conformations during substrates binding , 2000, The EMBO journal.

[50]  J. Perona,et al.  tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase. , 2003, Structure.

[51]  S Thirup,et al.  The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA. , 1999, Structure.

[52]  S. Brenner,et al.  Cysteinyl‐tRNA synthetase is a direct descendant of the first aminoacyl‐tRNA synthetase , 1991, FEBS letters.

[53]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[54]  R Giegé,et al.  The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules. , 2000, Structure.

[55]  T. Steitz,et al.  Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 A resolution. , 1989, Science.

[56]  S Cusack,et al.  The 2 Å crystal structure of leucyl‐tRNA synthetase and its complex with a leucyl‐adenylate analogue , 2000, The EMBO journal.

[57]  E. Westhof,et al.  An unusual RNA tertiary interaction has a role for the specific aminoacylation of a transfer RNA. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[58]  J. Perona,et al.  Alternative designs for construction of the class II transfer RNA tertiary core. , 2000, RNA.

[59]  Y. Hou,et al.  An RNA structural determinant for tRNA recognition. , 1997, Biochemistry.

[60]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[61]  A strategy of tRNA recognition that includes determinants of RNA structure. , 1997, Bioorganic & medicinal chemistry.

[62]  C. Carter,et al.  Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase. , 1995, Structure.