Escherichia coliTryptophanyl-tRNA Synthetase Mutants Selected for Tryptophan Auxotrophy Implicate the Dimer Interface in Optimizing Amino Acid Binding†

Biochemistry ◽  
1996 ◽  
Vol 35 (1) ◽  
pp. 32-40 ◽  
Author(s):  
Sanja Sever ◽  
Kelley Rogers ◽  
M. John Rogers ◽  
Charles Carter, ◽  
Dieter Söll
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Dimer Interface ◽  
Amino Acid Binding

scholarly journals Transcription and translation in an RNA world

2006 ◽  
Vol 361 (1474) ◽  
pp. 1751-1760 ◽  
Author(s):  
William R Taylor
Keyword(s):  
Amino Acid ◽  
Active Site ◽  
Rna World ◽  
Large Subunit ◽  
Trna Synthetase ◽  
Nucleoside Triphosphate ◽  
Amino Acid Binding ◽  
World Hypothesis ◽  
Protein Elongation ◽  
Rna World Hypothesis

The RNA world hypothesis requires a ribozyme that was an RNA-directed RNA polymerase (ribopolymerase). If such a replicase makes a reverse complementary copy of any sequence (including itself), in a simple RNA world, there is no mechanism to prevent self-hybridization. It is proposed that this can be avoided through the synthesis of a parallel complementary copy. The logical consequences of this are pursued and developed in a computer simulation, where the behaviour of the parallel copy is compared to the conventional reverse complementary copy. It is found that the parallel copy is more efficient at higher temperatures (up to 90°C). A model for the ribopolymerase, based on the core of the large subunit (LSU) of the ribosome, is described. The geometry of a potential active site for this ribopolymerase suggests that it contained a cavity (now occupied by the aminoacyl-tRNA) and that an amino acid binding in this might have ‘poisoned’ the ribopolymerase by cross-reacting with the nucleoside-triphosphate before polymerization could occur. Based on a similarity to the active site components of the class-I tRNA synthetase enzymes, it is proposed that the amino acid could become attached to the nascent RNA transcript producing a variety of aminoacylated tRNA-like products. Using base-pairing interactions, some of these molecules might cross-link two ribopolymerases, giving rise to a precursor of the modern ribosome. A hybrid dimer, half polymerase and half proto-ribosome, could account for mRNA translocation before the advent of protein elongation factors.

scholarly journals The isolation of a peptide from the catalytic domain of Bacillus stearothermophilus tryptophyl-tRNA synthetase. The interaction of Brown MX-5BR with tyrosyl-tRNA synthetase

1987 ◽  
Vol 243 (3) ◽  
pp. 701-707 ◽  
Author(s):  
J E C McArdell ◽  
C J Bruton ◽  
T Atkinson
Keyword(s):  
Amino Acid ◽  
Bacillus Stearothermophilus ◽  
Catalytic Domain ◽  
Competitive Inhibitor ◽  
Trna Synthetase ◽  
Apparent Dissociation Constant ◽  
Peptide Peak ◽  
Competitive Kinetics ◽  
Amino Acid Binding ◽  
Dissociation Constant Kd

Tryptophyl-tRNA synthetase is irreversibly inactivated by Procion Brown MX-5BR with an apparent dissociation constant (KD) of 8.8 microM and maximum rate of inactivation k3 0.192 s-1. The specificity of the interaction is supported by two previously reported observations. Firstly, Brown MX-5BR inactivation of tryptophyl-tRNA synthetase is inhibited by substrates, and secondly, the animated derivative of Brown MX-5BR is a competitive inhibitor of tryptophyl-tRNA synthetase with a Ki of 2 X 10(-4) M with respect to both tryptophan and ATP. Tryptic digestion of the dye-affinity-labelled enzyme and subsequent resolution of the peptides by h.p.l.c. yielded one major dye-peptide peak. Amino acid sequence analysis resulted in the identification of the dye-binding domain centred on lysine-178. Tyrosyl-tRNA synthetase is also inactivated by Procion Brown MX-5BR, and this inactivation is prevented by ATP but not by tyrosine. The interaction of tyrosyl-tRNA synthetase with hydroxylated Brown MX-5BR exhibited non-competitive kinetics with respect to the amino acid-binding site and competitive kinetics against ATP with a Ki of 6 X 10(-6) M.

scholarly journals Pyrrolysyl-tRNA Synthetase with a Unique Architecture Enhances the Availability of Lysine Derivatives in Synthetic Genetic Codes

Molecules ◽  
2018 ◽  
Vol 23 (10) ◽  
pp. 2460 ◽  
Author(s):  
Atsushi Yamaguchi ◽  
Fumie Iraha ◽  
Kazumasa Ohtake ◽  
Kensaku Sakamoto
Keyword(s):  
Amino Acid ◽  
Binding Pocket ◽  
Trna Synthetase ◽  
Aminoacyl Trna Synthetase ◽  
Genetic Codes ◽  
Genetic Code Expansion ◽  
Amino Acid Binding ◽  
Derivatives Of ◽  
Additional Nucleotide ◽  
Incorporation Efficiency

Genetic code expansion has largely relied on two types of the tRNA—aminoacyl-tRNA synthetase pairs. One involves pyrrolysyl-tRNA synthetase (PylRS), which is used to incorporate various lysine derivatives into proteins. The widely used PylRS from Methanosarcinaceae comprises two distinct domains while the bacterial molecules consist of two separate polypeptides. The recently identified PylRS from Candidatus Methanomethylophilus alvus (CMaPylRS) is a single-domain, one-polypeptide enzyme that belongs to a third category. In the present study, we showed that the PylRS—tRNAPyl pair from C. M. alvus can incorporate lysine derivatives much more efficiently (up to 14-times) than Methanosarcinaceae PylRSs in Escherichia coli cell-based and cell-free systems. Then we investigated the tRNA and amino-acid recognition by CMaPylRS. The cognate tRNAPyl has two structural idiosyncrasies: no connecting nucleotide between the acceptor and D stems and an additional nucleotide in the anticodon stem and it was found that these features are hardly recognized by CMaPylRS. Lastly, the Tyr126Ala and Met129Leu substitutions at the amino-acid binding pocket were shown to allow CMaPylRS to recognize various derivatives of the bulky Nε-benzyloxycarbonyl-l-lysine (ZLys). With the high incorporation efficiency and the amenability to engineering, CMaPylRS would enhance the availability of lysine derivatives in expanded codes.

The zinc-binding site of a class I aminoacyl-tRNA synthetase is a SWIM domain that modulates amino acid binding via the tRNA acceptor arm

2004 ◽  
Vol 271 (4) ◽  
pp. 724-733 ◽  
Author(s):  
Rajat Banerjee ◽  
Daniel Y. Dubois ◽  
Joelle Gauthier ◽  
Sheng-Xiang Lin ◽  
Siddhartha Roy ◽  
...  
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Trna Synthetase ◽  
Class I ◽  
Zinc Binding ◽  
Aminoacyl Trna Synthetase ◽  
Zinc Binding Site ◽  
Amino Acid Binding ◽  
Trna Acceptor

Thiol Ligation of Two Zinc Atoms to a Class I tRNA Synthetase: Evidence for Unshared Thiols and Role in Amino Acid Binding and Utilization

Biochemistry ◽  
1994 ◽  
Vol 33 (47) ◽  
pp. 14213-14220 ◽  
Author(s):  
James A. Landro ◽  
Eric Schmidt ◽  
Paul Schimmel ◽  
David L. Tierney ◽  
James E. Penner-Hahn
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Class I ◽  
Amino Acid Binding
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