Residues in a Class I tRNA Synthetase Which Determine Selectivity of Amino Acid Recognition in the Context of tRNA

Biochemistry ◽  
1995 ◽  
Vol 34 (35) ◽  
pp. 11204-11210 ◽  
Author(s):  
Eric Schmidt ◽  
Paul Schimmel
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Class I ◽  
Amino Acid Recognition

Structural Basis of Furan-Amino Acid Recognition by a Polyspecific Aminoacyl-tRNA-Synthetase and its Genetic Encoding in Human Cells

ChemBioChem ◽  
2014 ◽  
Vol 15 (12) ◽  
pp. 1755-1760 ◽  
Author(s):  
Moritz J. Schmidt ◽  
Annemarie Weber ◽  
Moritz Pott ◽  
Wolfram Welte ◽  
Daniel Summerer
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Human Cells ◽  
Structural Basis ◽  
Aminoacyl Trna Synthetase ◽  
Genetic Encoding ◽  
Amino Acid Recognition

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

Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations 1 1A. R. Fersht

1998 ◽  
Vol 275 (5) ◽  
pp. 823-846 ◽  
Author(s):  
Georgios Archontis ◽  
Thomas Simonson ◽  
Dino Moras ◽  
Martin Karplus
Keyword(s):  
Free Energy ◽  
Amino Acid ◽  
Trna Synthetase ◽  
Specific Amino Acid ◽  
Energy Simulations ◽  
Amino Acid Recognition

How methionyl-tRNA synthetase creates its amino acid recognition pocket upon l-methionine binding

2001 ◽  
Vol 306 (4) ◽  
pp. 863-876 ◽  
Author(s):  
Laurence Serre ◽  
Grégory Verdon ◽  
Thomas Choinowski ◽  
Nadège Hervouet ◽  
Jean-Loup Risler ◽  
...  
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Methionyl Trna Synthetase ◽  
Amino Acid Recognition

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.

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