Genomes and Genes
Gene Symbol: alaS
Description: alanyl-tRNA synthetase
Alias: ECK2692, JW2667, act, ala-act, lovB
Species: Escherichia coli str. K-12 substr. MG1655
- Buechter D, Schimmel P. Minor groove recognition of the critical acceptor helix base pair by an appended module of a class II tRNA synthetase. Biochemistry. 1995;34:6014-9 pubmed..A "fold-back" appendage provides a specific mechanism for minor groove recognition of the acceptor helix by a class II tRNA synthetase. ..
- McClain W, Foss K. Changing the identity of a tRNA by introducing a G-U wobble pair near the 3' acceptor end. Science. 1988;240:793-6 pubmed..The identity of the resulting tRNA, when examined as an amber suppressor in Escherichia coli, was that of tRNAAla. ..
- Hill K, Schimmel P. Evidence that the 3' end of a tRNA binds to a site in the adenylate synthesis domain of an aminoacyl-tRNA synthetase. Biochemistry. 1989;28:2577-86 pubmed
- Ibba M, Soll D. Aminoacyl-tRNA synthesis. Annu Rev Biochem. 2000;69:617-50 pubmed..This article reviews current knowledge of the biochemical, structural, and evolutionary facets of aminoacyl-tRNA synthesis. ..
- Lu Y, Hill K. The invariant arginine in motif 2 of Escherichia coli alanyl-tRNA synthetase is important for catalysis but not for substrate binding. J Biol Chem. 1994;269:12137-41 pubmed..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 ..
- Tsui W, Fersht A. Probing the principles of amino acid selection using the alanyl-tRNA synthetase from Escherichia coli. Nucleic Acids Res. 1981;9:4627-37 pubmed..The smaller amino acid glycine is also readily activated and its reaction products rapidly removed by hydrolytic editing. ..
- Romeo T, Gong M, Liu M, Brun Zinkernagel A. Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface properties. J Bacteriol. 1993;175:4744-55 pubmed..Computer-assisted data base searches failed to identify genes or proteins that are homologous with csrA or its gene product. ..
- Gabriel K, Schneider J, McClain W. Functional evidence for indirect recognition of G.U in tRNA(Ala) by alanyl-tRNA synthetase. Science. 1996;271:195-7 pubmed..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. ..
- McClain W, Jou Y, Bhattacharya S, Gabriel K, Schneider J. The reliability of in vivo structure-function analysis of tRNA aminoacylation. J Mol Biol. 1999;290:391-409 pubmed..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. ..
- Bouloc P, Jaffe A, D Ari R. The Escherichia coli lov gene product connects peptidoglycan synthesis, ribosomes and growth rate. EMBO J. 1989;8:317-23 pubmed
- Pleiss J, Wolfson A, Uhlenbeck O. Mapping contacts between Escherichia coli alanyl tRNA synthetase and 2' hydroxyls using a complete tRNA molecule. Biochemistry. 2000;39:8250-8 pubmed..Contacts at similar sites in the T-loop are seen in the cocrystal structure of tRNA(Ser) and Thermus thermophilus seryl-tRNA synthetase. ..
- Beebe K, Merriman E, Schimmel P. Structure-specific tRNA determinants for editing a mischarged amino acid. J Biol Chem. 2003;278:45056-61 pubmed..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. ..
- Shi J, Musier Forsyth K, Schimmel P. Region of a conserved sequence motif in a class II tRNA synthetase needed for transfer of an activated amino acid to an RNA substrate. Biochemistry. 1994;33:5312-8 pubmed..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. ..
- Kondo K, Wakabayashi S, Yagi T, Kagamiyama H. The complete amino acid sequence of aspartate aminotransferase from Escherichia coli: sequence comparison with pig isoenzymes. Biochem Biophys Res Commun. 1984;122:62-7 pubmed..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. ..
- Putney S, Schimmel P. An aminoacyl tRNA synthetase binds to a specific DNA sequence and regulates its gene transcription. Nature. 1981;291:632-5 pubmed..The amino acid effect is caused by direct association of the ligand with the synthetase, which in turn mediates tighter binding to the DNA. ..
- McClain W, Gabriel K, Schneider J. Specific function of a G.U wobble pair from an adjacent helical site in tRNA(Ala) during recognition by alanyl-tRNA synthetase. RNA. 1996;2:105-9 pubmed..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. ..
- Sood S, Slattery C, Filley S, Wu M, Hill K. Further characterization of Escherichia coli alanyl-tRNA synthetase. Arch Biochem Biophys. 1996;328:295-301 pubmed..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. ..
- Beebe K, Ribas De Pouplana L, Schimmel P. Elucidation of tRNA-dependent editing by a class II tRNA synthetase and significance for cell viability. EMBO J. 2003;22:668-75 pubmed..Thus, tRNA-dependent editing by AlaRS may have been critical for making the genetic code sufficiently accurate to generate the tree of life. ..
- Sood S, Hill K, Slattery C. Stability of Escherichia coli alanyl-tRNA synthetase quaternary structure under increased pressure. Arch Biochem Biophys. 1997;346:322-3 pubmed
- Fischer A, Beuning P, Musier Forsyth K. Identification of discriminator base atomic groups that modulate the alanine aminoacylation reaction. J Biol Chem. 1999;274:37093-6 pubmed..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. ..
- Beuning P, Yang F, Schimmel P, Musier Forsyth K. Specific atomic groups and RNA helix geometry in acceptor stem recognition by a tRNA synthetase. Proc Natl Acad Sci U S A. 1997;94:10150-4 pubmed..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. ..
- Chang K, Varani G, Bhattacharya S, Choi H, McClain W. Correlation of deformability at a tRNA recognition site and aminoacylation specificity. Proc Natl Acad Sci U S A. 1999;96:11764-9 pubmed..Fidelity is ensured because noncognate and inactive mutant tRNAs are bound in the active site in an incorrect conformation that reduces enzymatic activity. ..
- Miller W, Schimmel P. A retroviral-like metal binding motif in an aminoacyl-tRNA synthetase is important for tRNA recognition. Proc Natl Acad Sci U S A. 1992;89:2032-5 pubmed..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. ..
- Sood S, Wu M, Hill K, Slattery C. Characterization of zinc-depleted alanyl-tRNA synthetase from Escherichia coli: role of zinc. Arch Biochem Biophys. 1999;368:380-4 pubmed..Furthermore, urea denaturation experiments demonstrate the role of zinc in stabilization of AlaRS structure. ..
- Andersen E, Rosenblad M, Larsen N, Westergaard J, Burks J, Wower I, et al. The tmRDB and SRPDB resources. Nucleic Acids Res. 2006;34:D163-8 pubmed publisher..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...
- Wu M, Filley S, Xiong J, Lee J, Hill K. A cysteine in the C-terminal region of alanyl-tRNA synthetase is important for aminoacylation activity. Biochemistry. 1994;33:12260-6 pubmed..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. ..
- Hou Y, Francklyn C, Schimmel P. Molecular dissection of a transfer RNA and the basis for its identity. Trends Biochem Sci. 1989;14:233-7 pubmed..Instead a single base pair is a major determinant for the identity of this tRNA. Even a synthetic RNA microhelix with seven base pairs can be aminoacylated if it includes the major determinant. ..
- Herlihy W, Royal N, Biemann K, Putney S, Schimmel P. Mass spectra of partial protein hydrolysates as a multiple phase check for long polypeptides deduced from DNA sequences: NH2-terminal segment of alanine tRNA synthetase. Proc Natl Acad Sci U S A. 1980;77:6531-5 pubmed..This paper reports the sequence of the first 165 amino acids from the NH2 terminus. ..
- Beuning P, Nagan M, Cramer C, Musier Forsyth K, Gelpi J, Bashford D. Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair. RNA. 2002;8:659-70 pubmed..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. ..
- Hou Y, Schimmel P. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature. 1988;333:140-5 pubmed..Thus, as little as a single base pair can direct an amino acid to a specific transfer RNA. ..
- Ribas de Pouplana L, Buechter D, Sardesai N, Schimmel P. Functional analysis of peptide motif for RNA microhelix binding suggests new family of RNA-binding domains. EMBO J. 1998;17:5449-57 pubmed
- Ho C, Jasin M, Schimmel P. Amino acid replacements that compensate for a large polypeptide deletion in an enzyme. Science. 1985;229:389-93 pubmed..They also may reflect that progenitors of large aminoacyl-tRNA (transfer RNA) synthetases--one of which was used in these studies--were themselves much smaller. ..
- Jasin M, Schimmel P. Deletion of an essential gene in Escherichia coli by site-specific recombination with linear DNA fragments. J Bacteriol. 1984;159:783-6 pubmed..Cell viability is maintained by provision of the essential gene on a plasmid with a temperature-sensitive replicon, resulting in cells which have a temperature-sensitive phenotype. ..
- Regan L, Bowie J, Schimmel P. Polypeptide sequences essential for RNA recognition by an enzyme. Science. 1987;235:1651-3 pubmed..Fragments of alanine tRNA synthetase were created by in vitro manipulations of the cloned alaS gene and examined for their interaction with alanine-specific tRNA...
- Dulebohn D, Choy J, Sundermeier T, Okan N, Karzai A. Trans-translation: the tmRNA-mediated surveillance mechanism for ribosome rescue, directed protein degradation, and nonstop mRNA decay. Biochemistry. 2007;46:4681-93 pubmed..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. ..
- Putney S, Sauer R, Schimmel P. Purification and properties of alanine tRNA synthetase from Escherichia coli A tetramer of identical subunits. J Biol Chem. 1981;256:198-204 pubmed..These results also mean that, with respect to aminoacyl adenylate formation activity, each subunit in the native tetramer acts independently. ..
- Zhang C, Perona J, Ryu K, Francklyn C, Hou Y. Distinct kinetic mechanisms of the two classes of Aminoacyl-tRNA synthetases. J Mol Biol. 2006;361:300-11 pubmed..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. ..
- Putney S, Meléndez D, Schimmel P. Cloning, partial sequencing, and in vitro transcription of the gene for alanine tRNA synthetase. J Biol Chem. 1981;256:205-11 pubmed
- Murayama N, Shimizu H, Takiguchi S, Baba Y, Amino H, Horiuchi T, et al. 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 F. J Mol Biol. 1996;256:483-502 pubmed..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...
- Filley S, Hill K. Amino acid substitutions at position 73 in motif 2 of Escherichia coli alanyl-tRNA synthetase. Arch Biochem Biophys. 1993;307:46-51 pubmed..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. ..
- Hou Y, Schimmel P. Modeling with in vitro kinetic parameters for the elaboration of transfer RNA identity in vivo. Biochemistry. 1989;28:4942-7 pubmed..The results delineate some of the kinetic boundaries for the design and accommodation of tRNA sequence variations in the elaboration of identity in vivo. ..
- Putney S, Royal N, Neuman de Vegvar H, Herlihy W, Biemann K, Schimmel P. Primary structure of a large aminoacyl-tRNA synthetase. Science. 1981;213:1497-501 pubmed
- Buckel P, Piepersberg W, Bock A. Suppression of temperature-sensitive aminoacyl-tRNA synthetase mutations by ribosomal mutations: a possible mechanism. Mol Gen Genet. 1976;149:51-61 pubmedThe biochemical basis of suppression of a temperature-sensitive alanyl-tRNA synthetase (alaS) mutation by mutational alterations of the ribosome has been investigated...
- Tiwari N, Woods L, Haley R, Kight A, Goforth R, Clark K, et al. Identification and characterization of native proteins of Escherichia coli BL-21 that display affinity towards Immobilized Metal Affinity Chromatography and Hydrophobic Interaction Chromatography Matrices. Protein Expr Purif. 2010;70:191-5 pubmed publisher..coli strain(s) deficient in certain genomic proteins, and the design of an IMAC-HIC affinity tail for recombinant protein isolation based on the very proteins deleted from the genome. ..
- Jovanovic M, Lilic M, Janjusevic R, Jovanovic G, Savic D, Milija J. tRNA synthetase mutants of Escherichia coli K-12 are resistant to the gyrase inhibitor novobiocin. J Bacteriol. 1999;181:2979-83 pubmed..expand this list with mutations in rpoN (the gene for RNA polymerase subunit sigma54) and the tRNA synthetase genes alaS, argS, ileS, and leuS...
- Jasin M, Regan L, Schimmel P. Dispensable pieces of an aminoacyl tRNA synthetase which activate the catalytic site. Cell. 1984;36:1089-95 pubmed..This could be a mechanism to build efficiently large enzymes which integrate the catalytic sites with other previously shown functional roles. ..
- Jasin M, Regan L, Schimmel P. Two mutations in the dispensable part of alanine tRNA synthetase which affect the catalytic activity. J Biol Chem. 1985;260:2226-30 pubmed..allele was cloned from the genome by reciprocal recombination with a multicopy plasmid that contains segments of alaS which flank the respective mutations...
- McClain W, Chen Y, Foss K, Schneider J. Association of transfer RNA acceptor identity with a helical irregularity. Science. 1988;242:1681-4 pubmed..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. ..
- Park S, Miller W, Schimmel P. Synthetic peptide model of an essential region of an aminoacyl-tRNA synthetase. Biochemistry. 1990;29:9212-8 pubmed
- Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990;347:203-6 pubmed..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. ..
- Barends S, Wower J, Kraal B. Kinetic parameters for tmRNA binding to alanyl-tRNA synthetase and elongation factor Tu from Escherichia coli. Biochemistry. 2000;39:2652-8 pubmed..These observations can be interpreted to suggest that additional factors facilitate tmRNA binding to ribosomes. ..
- Theall G, Low K, Soll D. Suppression of a defective alanyl-tRNA synthetase in Escherichia coli: a compensatory mutation to high alanine affinity. Mol Gen Genet. 1977;156:221-7 pubmed..The alaS gene maps just counterclockwise from recA on the E. coli map (94% cotransduction frequency)...
- Miller W, Schimmel P. A metal-binding motif implicated in RNA recognition by an aminoacyl-tRNA synthetase and by a retroviral gene product. Mol Microbiol. 1992;6:1259-62 pubmed
- Ataide S, Ibba M. Small molecules: big players in the evolution of protein synthesis. ACS Chem Biol. 2006;1:285-97 pubmed..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. ..
- Cusack S, Hartlein M, Leberman R. Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases. Nucleic Acids Res. 1991;19:3489-98 pubmed
- Wolfson A, Uhlenbeck O. Modulation of tRNAAla identity by inorganic pyrophosphatase. Proc Natl Acad Sci U S A. 2002;99:5965-70 pubmed..These results partially reconcile the discrepancy between in vivo and in vitro analysis of tRNA(Ala) identity. ..
- Pawar K, Suma K, Seenivasan A, Kuncha S, Routh S, Kruparani S, et al. Role of D-aminoacyl-tRNA deacylase beyond chiral proofreading as a cellular defense against glycine mischarging by AlaRS. elife. 2017;6: pubmed publisher..Our study thus reveals a hitherto unknown function of DTD in cracking the universal mechanistic dilemma encountered by AlaRS, and its physiological importance. ..
- Park S, Schimmel P. Evidence for interaction of an aminoacyl transfer RNA synthetase with a region important for the identity of its cognate transfer RNA. J Biol Chem. 1988;263:16527-30 pubmed..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. ..
- Guo M, Chong Y, Beebe K, Shapiro R, Yang X, Schimmel P. The C-Ala domain brings together editing and aminoacylation functions on one tRNA. Science. 2009;325:744-7 pubmed publisher..In addition, C-Ala may have played an essential role in the evolution of AlaRSs by coupling aminoacylation to editing to prevent mistranslation. ..
- Davis M, Buechter D, Schimmel P. Functional dissection of a predicted class-defining motif in a class II tRNA synthetase of unknown structure. Biochemistry. 1994;33:9904-11 pubmed..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. ..
- Musier Forsyth K, Schimmel P. Functional contacts of a transfer RNA synthetase with 2'-hydroxyl groups in the RNA minor groove. Nature. 1992;357:513-5 pubmed..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. ..