Nucleotide Determinants for tRNA-Dependent Amino Acid Discrimination by a Class I tRNA Synthetase†

Biochemistry ◽  
1999 ◽  
Vol 38 (51) ◽  
pp. 16898-16903 ◽  
Author(s):  
Mark A. Farrow ◽  
Brian E. Nordin ◽  
Paul Schimmel
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Class I

scholarly journals Amino Acid-dependent Transfer RNA Affinity in a Class I Aminoacyl-tRNA Synthetase

2005 ◽  
Vol 280 (25) ◽  
pp. 23966-23977 ◽  
Author(s):  
Nathan T. Uter ◽  
Ita Gruic-Sovulj ◽  
John J. Perona
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Transfer Rna ◽  
Class I ◽  
Aminoacyl Trna Synthetase

Amino Acid Discrimination by a Class I Aminoacyl-tRNA Synthetase Specified by Negative Determinants

2003 ◽  
Vol 328 (2) ◽  
pp. 395-408 ◽  
Author(s):  
Timothy L. Bullock ◽  
Nathan Uter ◽  
T. Amar Nissan ◽  
John J. Perona
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Class I ◽  
Aminoacyl Trna Synthetase

scholarly journals Evidence that gene G7a in the human major histocompatibility complex encodes valyl-tRNA synthetase

1991 ◽  
Vol 278 (3) ◽  
pp. 809-816 ◽  
Author(s):  
S L Hsieh ◽  
R D Campbell
Keyword(s):  
Major Histocompatibility Complex ◽  
Amino Acid ◽  
Molecular Mass ◽  
Trna Synthetase ◽  
Class I ◽  
Major Histocompatibility ◽  
High Sequence Identity ◽  
Human Major Histocompatibility Complex ◽  
Trna Synthetases ◽  
Histocompatibility Complex

At least 36 genes have now been located in a 680 kb segment of DNA between the class I and class II multigene families within the class III region of the human major histocompatibility complex on chromosome 6p21.3. The complete nucleotide sequence of the 4.3 kb mRNA of one of these genes, G7a (or BAT6), has been determined from cDNA and genomic clones. The single-copy G7a gene encodes a 1265-amino-acid protein of molecular mass 140,457 Da. Comparison of the derived amino acid sequence of the G7a protein with the National Biomedical Research Foundation protein databases revealed 42% identity in a 250-amino-acid overlap with Bacillus stearothermophilus valyl-tRNA synthetase, 38.0% identity in a 993-amino-acid overlap with Escherichia coli valyl-tRNA synthetase (val RS), and 48.3% identity in a 1043-amino-acid overlap with Saccharomyces cerevisiae valyl-tRNA synthetase. The protein sequence of G7a contains two short consensus sequences, His-Ile-Gly-His and Lys-Met-Ser-Lys-Ser, which is the typical signature structure of class I tRNA synthetases and indicative of the presence of the Rossman fold. In addition, the molecular mass of the G7a protein is the same as that of other mammalian valyl-tRNA synthetases. These features and the high sequence identity with yeast valyl-tRNA synthetase strongly support the fact that the G7a gene, located within the major histocompatibility complex, encodes the human valyl-tRNA synthetase.

scholarly journals High-Resolution, Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-modular ‘Coupling

2020 ◽  
Author(s):  
Charles W. Carter ◽  
Alex Popinga ◽  
Remco Bouckaert ◽  
Peter R. Wills
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Class I ◽  
Evolutionary Divergence ◽  
Aminoacyl Trna Synthetase ◽  
Insertion Element ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Residue Conservation ◽  
Genetic Coding

AbstractThe provenance of the aminoacyl-tRNA synthetases (aaRS) poses unusually challenging questions because of their role in the emergence and evolution of genetic coding. We investigate evidence about their ancestry from highly curated structure-based multiple sequence alignments of a small “scaffold” that is structurally invariant in all 10 canonical Class I aaRS. Statistically different values of two uncorrelated phylogenetic metrics—residue by residue conservation derived from Clustal and row-by-row cladistic congruence derived from BEAST2—suggest that the Class I scaffold is a mosaic assembled from distinct, successive genetic sources. These data are especially significant in light of: (i) experimental fragmentations of the Class I scaffold into three partitions that retain catalytic activities in proportion to their length; and (ii) multiple sources of evidence that two of these partitions arose from an ancestral Class I aaRS gene encoding a Class II ancestor in frame on the opposite strand. Two additional metrics output by BEAST2 vary in accordance with the presumed functionality endowed by the various modules. The new evidence supplements previous aaRS phylogenies. It identifies a previously characterized 46-residue Class I “protozyme” as preceding the adaptive radiation of the superfamily containing variations of the Rossmann dinucleotide binding fold related to amino acid discrimination, and thus as root of that molecular tree. Such a rooting is consistent with near simultaneous emergence of genetic coding and the origin of the proteome, resolving a conundrum posed by previous inferences that Class I aaRS evolved long after the genetic code had been implemented in an RNA world. Further, it establishes a timeline for the growth of coding from a binary amino acid alphabet by pinpointing discontinuous enhancements of aaRS fidelity.Author SummaryPhylogenetic analysis uncovers evolutionary connections between different protein superfamily members. We describe complementary, uncorrelated, phylogenetic metrics that support multiple evolutionary histories for different segments within members of the Class I aminoacyl-tRNA synthetase superfamily. Using a carefully curated 3D crystal structure superposition as the primary source of the multiple sequence alignment substantially reduced dependence of these metrics on empirical amino acid substitution matrices. Two metrics are derived from the amino acid distribution observed in each successive position. A third depends on how individual sequences distribute into phylogenetic tree branches for each of the ten amino acids activated by the superfamily. All metrics confirm that a segment previously identified as an inserted element is, indeed, a more recent acquisition, despite its structural conservation. The residue-by-residue conservation metrics reveal significant co-variation of mutational frequencies between a core segment that forms the amino acid binding site and a neighboring segment derived from the more recent insertion element. We attribute that covariation to the differentiation of superfamily members as evolutionary divergence enhanced amino acid specificity. Finally, evidence that the insertion element is a recent acquisition implies a new branching order for much of the proteome.

scholarly journals The fidelity of the translation of the genetic code.

2001 ◽  
Vol 48 (2) ◽  
pp. 323-335 ◽  
Author(s):  
R Sankaranarayanan ◽  
D Moras
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Structural Information ◽  
Class Ii ◽  
Zinc Ion ◽  
Trna Synthetase ◽  
Class I ◽  
Structural Basis ◽  
Clear Understanding

Aminoacyl-tRNA synthetases play a central role in maintaining accuracy during the translation of the genetic code. To achieve this challenging task they have to discriminate against amino acids that are very closely related not only in structure but also in chemical nature. A 'double-sieve' editing model was proposed in the late seventies to explain how two closely related amino acids may be discriminated. However, a clear understanding of this mechanism required structural information on synthetases that are faced with such a problem of amino acid discrimination. The first structural basis for the editing model came recently from the crystal structure of isoleucyl-tRNA synthetase, a class I synthetase, which has to discriminate against valine. The structure showed the presence of two catalytic sites in the same enzyme, one for activation, a coarse sieve which binds both isoleucine and valine, and another for editing, a fine sieve which binds only valine and rejects isoleucine. Another structure of the enzyme in complex with tRNA showed that the tRNA is responsible for the translocation of the misactivated amino-acid substrate from the catalytic site to the editing site. These studies were mainly focused on class I synthetases and the situation was not clear about how class II enzymes discriminate against similar amino acids. The recent structural and enzymatic studies on threonyl-tRNA synthetase, a class II enzyme, reveal how this challenging task is achieved by using a unique zinc ion in the active site as well as by employing a separate domain for specific editing activity. These studies led us to propose a model which emphasizes the mirror symmetrical approach of the two classes of enzymes and highlights that tRNA is the key player in the evolution of these class of enzymes.

scholarly journals Arginyl-tRNA synthetase with signature sequence KMSK from Bacillus stearothermophilus

2003 ◽  
Vol 376 (3) ◽  
pp. 773-779 ◽  
Author(s):  
Juan LI ◽  
Yong-Neng YAO ◽  
Mo-Fang LIU ◽  
En-Duo WANG
Keyword(s):  
Amino Acid ◽  
Bacillus Stearothermophilus ◽  
Genomic Sequence ◽  
Trna Synthetase ◽  
Class I ◽  
Acid Activation ◽  
Gene Encoding ◽  
Mutual Compensation ◽  
Nickel Affinity Chromatography ◽  
High Loop

ArgRS (arginyl-tRNA synthetase) belongs to the class I aaRSs (aminoacyl-tRNA synthetases), though the majority of ArgRS species lack the canonical KMSK sequence characteristic of class I aaRSs. A DNA fragment of the ArgRS gene from Bacillus stearothermophilus was amplified using primers designed according to the conserved regions of known ArgRSs. Through analysis of the amplified DNA sequence and known tRNAArgs with a published genomic sequence of B. stearothermophilus, the gene encoding ArgRS (argS´) was amplified by PCR and the gene encoding tRNAArg (ACG) was synthesized. ArgRS contained 557 amino acid residues including the canonical KMKS sequence. Recombinant ArgRS and tRNAArg (ACG) were expressed in Escherichia coli. ArgRS purified by nickel-affinity chromatography had no ATPase activity. The kinetics of ArgRS and cross-recognition between ArgRSs and tRNAArgs from B. stearothermophilus and E. coli were studied. The activities of B. stearothermophilus ArgRS mutated at Lys382 and Lys385 of the KMSK sequence and at Gly136 upstream of the HIGH loop were determined. From the mutation results, we concluded that there was mutual compensation of Lys385 and Gly136 for the amino acid-activation activity of B. stearothermophilus ArgRS.

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
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