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

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

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 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 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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