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Genomes and Genes | alaSSummaryGene Symbol: alaS Description: alanyl-tRNA synthetase Alias: ECK2692, JW2667, act, ala-act, lovB Species: Top Publications
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Distinct domains of tRNA synthetase recognize the same base pairKirk Beebe
Department of Molecular Biology and Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
Nature 451:90-3. 2008..These also recognize mischarged tRNA(Ala). Thus, through evolution, three different complexes with the same tRNA can guard against mistaking glycine or serine for alanine...- Specific atomic groups and RNA helix geometry in acceptor stem recognition by a tRNA synthetaseP J Beuning
Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
Proc Natl Acad Sci U S A 94:10150-4. 1997..By implication, the activity of mutant tRNAs measured in the in vivo assays appears to be more dependent on factors other than aminoacylation kinetic efficiency... - Further characterization of Escherichia coli alanyl-tRNA synthetaseS M Sood
Department of Biochemistry, Loma Linda University School of Medicine, California 92350 0001, USA
Arch Biochem Biophys 328:295-301. 1996..The isoelectric point was determined experimentally to be 4.9. Sedimentation equilibrium data were best fit to a decamer association complex in which dimeric AlaRS is the predominant species at 25 degrees C... - Evidence for involvement of Escherichia coli genes pmbA, csrA and a previously unrecognized gene tldD, in the control of DNA gyrase by letD (ccdB) of sex factor FN Murayama
Faculty of Pharmaceutical Sciences, Kyushu Univrsity, Fukuoka, Japan
J Mol Biol 256:483-502. 1996..interaction between the LetD protein and the A subunit of DNA gyrase, while the tldD, tldE and groE gene products act to suppress the inhibitory activity of the zfiA gene product. The tldD, tldE, and zfiA genes are located at 70... - Specific function of a G.U wobble pair from an adjacent helical site in tRNA(Ala) during recognition by alanyl-tRNA synthetaseW H McClain
Department of Bacteriology, University of Wisconsin, Madison 53706 1567, USA
RNA 2:105-9. 1996..We find, as in the original experiment, that a shifted G.U confers Ala acceptor activity. Moreover, the modified tRNA(Lys) was specific for Ala, corroborating our original conclusion and making it more compelling... - Functional evidence for indirect recognition of G.U in tRNA(Ala) by alanyl-tRNA synthetaseK Gabriel
Department of Bacteriology, University of Wisconsin, Madison 53706, USA
Science 271:195-7. 1996..coli lacking chromosomal tRNA(Ala) genes. tRNA(Ala) with G.C was inactive. Recognition of G.U by AlaRS thus requires more than the functional groups on G.U in a regular helix and may involve detection of a helical distortion... - Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface propertiesT Romeo
Department of Microbiology and Immunology, University of North Texas, Fort Worth 76107 2699
J Bacteriol 175:4744-55. 1993..Computer-assisted data base searches failed to identify genes or proteins that are homologous with csrA or its gene product... - Amino acid substitutions at position 73 in motif 2 of Escherichia coli alanyl-tRNA synthetaseS J Filley
Department of Biochemistry, Loma Linda University School of Medicine, California 92350
Arch Biochem Biophys 307:46-51. 1993..Hartlein, M., and Leberman, R. (1991) Nucleic Acids Res. 19, 3489-3498], but question the predicted alignment of this motif with other enzymes in its class... - Region of a conserved sequence motif in a class II tRNA synthetase needed for transfer of an activated amino acid to an RNA substrateJ P Shi
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 33:5312-8. 1994..Because D235 in alanine tRNA synthetase is at the beginning of one of the conserved motifs that define class II tRNA synthetases, this region of the structure may in general be important for the transfer step... - The invariant arginine in motif 2 of Escherichia coli alanyl-tRNA synthetase is important for catalysis but not for substrate bindingY Lu
Department of Biochemistry, Loma Linda University School of Medicine, California 92350
J Biol Chem 269:12137-41. 1994..In this set, only mutations at position 69 caused the enzyme to lose ability to complement growth of an alaS deletion strain, and proteins containing substitutions at position 69 alone are undetectable in a Western blot .. - Functional dissection of a predicted class-defining motif in a class II tRNA synthetase of unknown structureM W Davis
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 33:9904-11. 1994..The results suggest that similar analyses will be generally useful in testing models for active site regions of other class II aminoacyl-tRNA synthetases of unknown structure... - A cysteine in the C-terminal region of alanyl-tRNA synthetase is important for aminoacylation activityM X Wu
Department of Biochemistry, Loma Linda University School of Medicine, California 92350
Biochemistry 33:12260-6. 1994..8) with respect to the RNA substrate. The results demonstrate that a simple manipulation in the C-terminal region can introduce positive cooperativity in this otherwise noncooperative enzyme... - Minor groove recognition of the critical acceptor helix base pair by an appended module of a class II tRNA synthetaseD D Buechter
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
Biochemistry 34:6014-9. 1995..A "fold-back" appendage provides a specific mechanism for minor groove recognition of the acceptor helix by a class II tRNA synthetase... - Functional analysis of peptide motif for RNA microhelix binding suggests new family of RNA-binding domainsL Ribas de Pouplana
The Skaggs Institute for Chemical Biology and Departments of Molecular Biology and Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
EMBO J 17:5449-57. 1998.... - tRNA synthetase mutants of Escherichia coli K-12 are resistant to the gyrase inhibitor novobiocinM Jovanovic
Institute of Molecular Genetics and Genetic Engineering, 11001 Belgrade, Yugoslavia
J Bacteriol 181:2979-83. 1999..expand this list with mutations in rpoN (the gene for RNA polymerase subunit sigma54) and the tRNA synthetase genes alaS, argS, ileS, and leuS... - The reliability of in vivo structure-function analysis of tRNA aminoacylationW H McClain
Department of Bacteriology, University of Wisconsin, Madison, WI, 53706 1567, USA
J Mol Biol 290:391-409. 1999..These experiments support the authenticity of the cellular assay and imply that a condition or factor present in the cell assay may be absent in the test tube assay... - Trans-translation: the tmRNA-mediated surveillance mechanism for ribosome rescue, directed protein degradation, and nonstop mRNA decayDaniel Dulebohn
Department of Biochemistry and Cell Biology and The Center for Infectious Diseases, Stony Brook University, Stony Brook, New York 11794, USA
Biochemistry 46:4681-93. 2007..This review will focus on recent advances in our understanding of the structural properties, mechanistic details, and physiological significance of this unique RNA and its principal protein partners... - Small molecules: big players in the evolution of protein synthesisSandro F Ataide
Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
ACS Chem Biol 1:285-97. 2006..Here, we discuss discrimination of small molecules by aaRSs, and how the evolutionary divergence of these mechanisms offers a means to target inhibitors against these essential microbial enzymes... - Distinct kinetic mechanisms of the two classes of Aminoacyl-tRNA synthetasesChun Mei Zhang
Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
J Mol Biol 361:300-11. 2006..These results emphasize that the distinct mechanistic signatures of class I versus class II tRNA synthetases ensure rapid turnover of aminoacyl-tRNAs during protein synthesis... - The tmRDB and SRPDB resourcesEbbe Sloth Andersen
Department of Molecular Biology, University of Aarhus, C F Moellers Alle, Building 139, 8000 Aarhus, Denmark
Nucleic Acids Res 34:D163-8. 2006..All alignments can be easily examined using a new exploratory browser. The databases provide links to high-resolution structures and serve as depositories for structures obtained by molecular modeling... - Structure-specific tRNA determinants for editing a mischarged amino acidKirk Beebe
Department of Molecular Biology and Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
J Biol Chem 278:45056-61. 2003..Because errors of aminoacylation are known to be deleterious to cell growth, structure-specific determinants constitute a powerful selective pressure to retain the format of the two-domain L-shaped tRNA... - Elucidation of tRNA-dependent editing by a class II tRNA synthetase and significance for cell viabilityKirk Beebe
The Skaggs Institute for Chemical Biology, The Scripps Research Institute, Beckman Center, BCC379, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
EMBO J 22:668-75. 2003..Thus, tRNA-dependent editing by AlaRS may have been critical for making the genetic code sufficiently accurate to generate the tree of life... - Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pairPenny J Beuning
Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis 55455 0431, USA
RNA 8:659-70. 2002..This analysis revealed a positive correlation between major groove negative electrostatic potential in the vicinity of the 3:70 base pair and measured aminoacylation efficiency... - Modulation of tRNAAla identity by inorganic pyrophosphataseAlexey D Wolfson
Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309 0215, USA
Proc Natl Acad Sci U S A 99:5965-70. 2002..These results partially reconcile the discrepancy between in vivo and in vitro analysis of tRNA(Ala) identity... - Aminoacyl-tRNA synthesisM Ibba
Center for Biomolecular Recognition, IMBG Laboratory B, The Panum Institute, DK 2200, Copenhagen N, Denmark
Annu Rev Biochem 69:617-50. 2000..This article reviews current knowledge of the biochemical, structural, and evolutionary facets of aminoacyl-tRNA synthesis... - Importance of discriminator base stacking interactions: molecular dynamics analysis of A73 microhelix(Ala) variantsM C Nagan
Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis 55455 0431, USA
Nucleic Acids Res 28:2527-34. 2000.... - Identification of discriminator base atomic groups that modulate the alanine aminoacylation reactionA E Fischer
Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
J Biol Chem 274:37093-6. 1999..Taken together, these new results are consistent with the involvement of major groove atomic groups of the discriminator base in the formation of the transition state for the amino acid transfer step... - Correlation of deformability at a tRNA recognition site and aminoacylation specificityK Y Chang
Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, United Kingdom
Proc Natl Acad Sci U S A 96:11764-9. 1999..Fidelity is ensured because noncognate and inactive mutant tRNAs are bound in the active site in an incorrect conformation that reduces enzymatic activity... - Characterization of zinc-depleted alanyl-tRNA synthetase from Escherichia coli: role of zincS M Sood
Department of Biochemistry, Loma Linda University School of Medicine, Loma Linda, California, 92350, USA
Arch Biochem Biophys 368:380-4. 1999..Furthermore, urea denaturation experiments demonstrate the role of zinc in stabilization of AlaRS structure... - Primary structure of a large aminoacyl-tRNA synthetaseS D Putney
Science 213:1497-501. 1981 - Mass spectra of partial protein hydrolysates as a multiple phase check for long polypeptides deduced from DNA sequences: NH2-terminal segment of alanine tRNA synthetaseW C Herlihy
Proc Natl Acad Sci U S A 77:6531-5. 1980..This paper reports the sequence of the first 165 amino acids from the NH2 terminus... - Association of transfer RNA acceptor identity with a helical irregularityW H McClain
Department of Bacteriology, University of Wisconsin, Madison 53706
Science 242:1681-4. 1988..These results suggest that the G.U wobble pair induces an irregularity in the acceptor helix of tRNA(Ala) to match a complementary structure in the aminoacylating enzyme... - Changing the identity of a tRNA by introducing a G-U wobble pair near the 3' acceptor endW H McClain
Department of Bacteriology, University of Wisconsin, Madison 53706
Science 240:793-6. 1988..The identity of the resulting tRNA, when examined as an amber suppressor in Escherichia coli, was that of tRNAAla... - Synthetic peptide model of an essential region of an aminoacyl-tRNA synthetaseS J Park
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 29:9212-8. 1990.... - Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifsG Eriani
Laboratoires de Biochimie, IBMC du CNRS, Strasbourg, France
Nature 347:203-6. 1990..Surprisingly, this partition of aaRS in two classes is found to be strongly correlated on the functional level with the acylation occurring either on the 2' OH (class I) or 3' OH (class II) of the ribose of the last nucleotide of tRNA... - Mutant aminoacyl-tRNA synthetase that compensates for a mutation in the major identity determinant of its tRNAW T Miller
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 30:2635-41. 1991..The results demonstrate the capacity of an aminoacyl-tRNA synthetase to compensate through a single amino acid substitution for mutations in the major determinant of its cognate tRNA... - Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetasesS Cusack
European Molecular Biology Laboratory, Grenoble, France
Nucleic Acids Res 19:3489-98. 1991.... - Evidence for a "cysteine-histidine box" metal-binding site in an Escherichia coli aminoacyl-tRNA synthetaseW T Miller
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 30:6970-6. 1991.... - Aminoacylation of alanine minihelices. "Discriminator" base modulates transition state of single turnover reactionJ P Shi
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
J Biol Chem 266:2705-8. 1991..The results suggest that the nature of the discriminator base is a critical determinant of the transition state for the reaction of bound alanyl adenylate with RNA on the surface of the enzyme... - A nucleotide that enhances the charging of RNA minihelix sequence variants with alanineJ P Shi
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 29:3621-6. 1990..Comparison with earlier work suggests that the substantial modulating effect of N73 is partly or completely obscured when N73 tRNA variants are expressed as amber suppressors in vivo... - Functional contacts of a transfer RNA synthetase with 2'-hydroxyl groups in the RNA minor grooveK Musier-Forsyth
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
Nature 357:513-5. 1992..U70 base pair and find that functional 2'-hydroxyl contacts are clustered within a few ångstroms of the critical 2-amino group. These contacts are highly specific and make a thermodynamically significant contribution to RNA recognition... - A retroviral-like metal binding motif in an aminoacyl-tRNA synthetase is important for tRNA recognitionW T Miller
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
Proc Natl Acad Sci U S A 89:2032-5. 1992..These and additional experiments collectively suggest a role for the retroviral-like metal binding motif in RNA recognition and, further, raise the possibility that the protein-bound metal itself participates in an RNA interaction... - A metal-binding motif implicated in RNA recognition by an aminoacyl-tRNA synthetase and by a retroviral gene productW T Miller
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
Mol Microbiol 6:1259-62. 1992.... - The Escherichia coli lov gene product connects peptidoglycan synthesis, ribosomes and growth rateP Bouloc
Institut Jacques Monod, Centre National de la Recherche Scientifique, Universite Paris, France
EMBO J 8:317-23. 1989.... - Evidence that the 3' end of a tRNA binds to a site in the adenylate synthesis domain of an aminoacyl-tRNA synthetaseK Hill
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 28:2577-86. 1989.... - Modeling with in vitro kinetic parameters for the elaboration of transfer RNA identity in vivoY M Hou
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 28:4942-7. 1989..The results delineate some of the kinetic boundaries for the design and accommodation of tRNA sequence variations in the elaboration of identity in vivo... - The complete amino acid sequence of aspartate aminotransferase from Escherichia coli: sequence comparison with pig isoenzymesK Kondo
Biochem Biophys Res Commun 122:62-7. 1984..coli enzyme exhibited the same degree of homology (about 40%) with either of them. Although majority of the residues were substituted, the functional residues constituting the active site structure were conserved... - Cloning, partial sequencing, and in vitro transcription of the gene for alanine tRNA synthetaseS D Putney
J Biol Chem 256:205-11. 1981 - Selection of temperature-sensitive activating enzyme mutants in Escherichia coliS Kaplan
J Bacteriol 95:991-7. 1968..In the latter instance, an increased proportion of temperature-sensitive macromolecule mutants of other types is obtained. Additional uses of this procedure are discussed... - Evidence for interaction of an aminoacyl transfer RNA synthetase with a region important for the identity of its cognate transfer RNAS J Park
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
J Biol Chem 263:16527-30. 1988..There is no evidence for interaction of the enzyme with the anticodon, a sequence which can be varied without effect on recognition by alanine tRNA synthetase... - Mapping contacts between Escherichia coli alanyl tRNA synthetase and 2' hydroxyls using a complete tRNA moleculeJ A Pleiss
Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
Biochemistry 39:8250-8. 2000..Contacts at similar sites in the T-loop are seen in the cocrystal structure of tRNA(Ser) and Thermus thermophilus seryl-tRNA synthetase... - Acceptor helix interactions in a class II tRNA synthetase: photoaffinity cross-linking of an RNA miniduplex substrateK Musier Forsyth
Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
Biochemistry 33:773-9. 1994..The sequence diversity of this segment implies that its mode of interaction with the acceptor helix is idiosyncratic to the class II enzyme... - Kinetic parameters for tmRNA binding to alanyl-tRNA synthetase and elongation factor Tu from Escherichia coliS Barends
Department of Biochemistry, Leiden Institute of Chemistry, Leiden University, P O Box 9502, 2300 RA Leiden, The Netherlands
Biochemistry 39:2652-8. 2000..These observations can be interpreted to suggest that additional factors facilitate tmRNA binding to ribosomes... - Construction of a contiguous 874-kb sequence of the Escherichia coli -K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence featuresY Yamamoto
Department of Genetics, Hyogo College of Medicine, Nishinomiya, Japan
DNA Res 4:91-113. 1997..An isoleucine tRNA gene, designated ileY, was also newly identified at 60.0 min...