Role for a Conserved Structural Motif in Assembly of a Class I Aminoacyl-tRNA Synthetase Active Site

Biochemistry ◽  
2011 ◽  
Vol 50 (5) ◽  
pp. 763-769 ◽  
Author(s):  
Veronica C. Casina ◽  
Andrew A. Lobashevsky ◽  
William E. McKinney ◽  
Cassidy L. Brown ◽  
Rebecca W. Alexander
Keyword(s):  
Active Site ◽  
Trna Synthetase ◽  
Class I ◽  
Structural Motif ◽  
Aminoacyl Trna Synthetase

scholarly journals tRNA-Dependent Active Site Assembly in a Class I Aminoacyl-tRNA Synthetase

Structure ◽  
2003 ◽  
Vol 11 (5) ◽  
pp. 591-603 ◽  
Author(s):  
Luke D Sherlin ◽  
John J Perona
Keyword(s):  
Active Site ◽  
Trna Synthetase ◽  
Class I ◽  
Aminoacyl Trna Synthetase

Active Site Nanospace of Aminoacyl tRNA Synthetase: Difference Between the Class I and Class II Synthetases

2014 ◽  
Vol 14 (3) ◽  
pp. 2280-2298 ◽  
Author(s):  
Saheb Dutta ◽  
Kaberi Choudhury ◽  
Sindrila Dutta Banik ◽  
Nilashis Nandi
Keyword(s):  
Active Site ◽  
Class Ii ◽  
Trna Synthetase ◽  
Class I ◽  
Aminoacyl Trna Synthetase

scholarly journals The relationship between synthetic and editing functions of the active site of an aminoacyl-tRNA synthetase.

1993 ◽  
Vol 90 (24) ◽  
pp. 11553-11557 ◽  
Author(s):  
H. Y. Kim ◽  
G. Ghosh ◽  
L. H. Schulman ◽  
S. Brunie ◽  
H. Jakubowski
Keyword(s):  
Active Site ◽  
Trna Synthetase ◽  
Aminoacyl Trna Synthetase ◽  
The Relationship

The Human EPRS Locus (Formerly the QARS Locus): A Gene Encoding a Class I and a Class II Aminoacyl-tRNA Synthetase

Genomics ◽  
1994 ◽  
Vol 19 (2) ◽  
pp. 280-290 ◽  
Author(s):  
Eva Kaiser ◽  
Bing Hu ◽  
Stefanie Becher ◽  
Dirk Eberhard ◽  
Beate Schray ◽  
...  
Keyword(s):  
Class Ii ◽  
Trna Synthetase ◽  
Class I ◽  
Aminoacyl Trna Synthetase ◽  
Gene Encoding

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 Ribosome Structure, Function, and Early Evolution

2018 ◽  
Vol 20 (1) ◽  
pp. 40 ◽  
Author(s):  
Kristopher Opron ◽  
Zachary Burton
Keyword(s):  
Molecular Motors ◽  
Ribonucleic Acid ◽  
Class Ii ◽  
Trna Synthetase ◽  
The Body ◽  
Class I ◽  
Aminoacyl Trna Synthetase ◽  
Messenger Ribonucleic Acid ◽  
Archaeal Species ◽  
30S Subunit

Ribosomes are among the largest and most dynamic molecular motors. The structure and dynamics of translation initiation and elongation are reviewed. Three ribosome motions have been identified for initiation and translocation. A swivel motion between the head/beak and the body of the 30S subunit was observed. A tilting dynamic of the head/beak versus the body of the 30S subunit was detected using simulations. A reversible ratcheting motion was seen between the 30S and the 50S subunits that slide relative to one another. The 30S–50S intersubunit contacts regulate translocation. IF2, EF-Tu, and EF-G are homologous G-protein GTPases that cycle on and off the same site on the ribosome. The ribosome, aminoacyl-tRNA synthetase (aaRS) enzymes, transfer ribonucleic acid (tRNA), and messenger ribonucleic acid (mRNA) form the core of information processing in cells and are coevolved. Surprisingly, class I and class II aaRS enzymes, with distinct and incompatible folds, are homologs. Divergence of class I and class II aaRS enzymes and coevolution of the genetic code are described by analysis of ancient archaeal species.

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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