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AlaS DNA-binding transcriptional repressor

Synonyms: AlaS-L-alanine, AlaS
Summary:
Alanine—tRNA ligase (AlaRS) is a member of the family of aminoacyl-tRNA synthetases, which interpret the genetic code by covalently linking amino acids to their specific tRNA molecules. The reaction is driven by ATP hydrolysis. AlaRS belongs to the Class IIC aminoacyl tRNA synthetases [2, 3, 4]. AlaRS was seen as a homotetramer in solution [5]. Later experiments determined that AlaRS is homodimeric in solution [6] and can exist in an equilibrium between a homodimeric and a homodecameric state, depending on temperature [7, 8]. The enzyme contains one molecule of zinc per AlaS polypeptide [9]; zinc binds cooperatively and induces a conformational change in AlaRS [10, 11].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
AlaS Non-Functional   Apo [BPP] [1]
AlaS-L-alanine Functional Allosteric Holo [APPHINH], [BPP], [HIFS], [IEP] [1]
Evolutionary Family: Class II aminoacyl_tRNA synthetase
Connectivity class: Local Regulator
Gene name: alaS
  Genome position: 2819381-2822011
  Length: 2631 bp / 876 aa
Operon name: alaS
TU(s) encoding the TF:
Transcription unit        Promoter
alaS
alaSp


Regulon       
Regulated gene(s) alaS
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
amino acid -activation (1)
repressor (1)
Regulated operon(s) alaS
First gene in the operon(s) alaS
Simple and complex regulons AlaS
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[AlaS,-](1)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  AlaS-L-alanine repressor alaSp nd -6.5 -86.0 alaS
ttacttcccaGTCAAGAAAACTTATCTTATTCCCACTTTTCAGTTaccagcccgg
2822080 2822114 [BPP], [GEA] [1]


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
Promoter-target gene evolutionary conservation


Evidence    

 [BPP] Binding of purified proteins

 [APPHINH] Assay of protein purified to homogeneity from its native host

 [HIFS] Human inference of function from sequence

 [IEP] Inferred from expression pattern

 [GEA] Gene expression analysis



Reference(s)    

 [1] Putney SD., Schimmel P., 1981, An aminoacyl tRNA synthetase binds to a specific DNA sequence and regulates its gene transcription., Nature 291(5817):632-5

 [2] Eriani G, Delarue M, Poch O, Gangloff J, Moras D, 1990, Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs., Nature, 1990 Sep 13

 [3] Cusack S, Härtlein M, Leberman R, 1991, Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases., Nucleic Acids Res, 1991 Jul 11

 [4] Perona JJ, Hadd A, 2012, Structural diversity and protein engineering of the aminoacyl-tRNA synthetases., Biochemistry, 2012 Nov 6

 [5] Putney SD, Sauer RT, Schimmel PR, 1981, Purification and properties of alanine tRNA synthetase from Escherichia coli A tetramer of identical subunits., J Biol Chem, 1981 Jan 10

 [6] Dignam JD, Guo J, Griffith WP, Garbett NC, Holloway A, Mueser T, 2011, Allosteric interaction of nucleotides and tRNA(ala) with E. coli alanyl-tRNA synthetase., Biochemistry, 2011 Nov 15

 [7] Sood SM, Slattery CW, Filley SJ, Wu MX, Hill KA, 1996, Further characterization of Escherichia coli alanyl-tRNA synthetase., Arch Biochem Biophys, 1996 Apr 15

 [8] Sood SM, Hill KA, Slattery CW, 1997, Stability of Escherichia coli alanyl-tRNA synthetase quaternary structure under increased pressure., Arch Biochem Biophys, 1997 Oct 15

 [9] Miller WT, Hill KA, Schimmel P, 1991, Evidence for a "cysteine-histidine box" metal-binding site in an Escherichia coli aminoacyl-tRNA synthetase., Biochemistry, 1991 Jul 16

 [10] Wu MX, Filley SJ, Hill KA, 1994, Cooperative binding of zinc to an aminoacyl-tRNA synthetase., Biochem Biophys Res Commun, 1994 Jun 30

 [11] Sood SM, Wu MX, Hill KA, Slattery CW, 1999, Characterization of zinc-depleted alanyl-tRNA synthetase from Escherichia coli: role of zinc., Arch Biochem Biophys, 1999 Aug 15

 [12] Miller WT, Schimmel P, 1992, A retroviral-like metal binding motif in an aminoacyl-tRNA synthetase is important for tRNA recognition., Proc Natl Acad Sci U S A, 1992 Mar 15

 [13] Park SJ, Schimmel P, 1988, 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 Nov 15

 [14] Gabriel K, Schneider J, McClain WH, 1996, Functional evidence for indirect recognition of G.U in tRNA(Ala) by alanyl-tRNA synthetase., Science, 1996 Jan 12

 [15] McClain WH, Gabriel K, Schneider J, 1996, Specific function of a G.U wobble pair from an adjacent helical site in tRNA(Ala) during recognition by alanyl-tRNA synthetase., RNA, 1996 Feb

 [16] McClain WH, Jou YY, Bhattacharya S, Gabriel K, Schneider J, 1999, The reliability of in vivo structure-function analysis of tRNA aminoacylation., J Mol Biol, 1999 Jul 9

 [17] Pleiss JA, Wolfson AD, Uhlenbeck OC, 2000, Mapping contacts between Escherichia coli alanyl tRNA synthetase and 2' hydroxyls using a complete tRNA molecule., Biochemistry, 2000 Jul 18

 [18] Wolfson AD, Uhlenbeck OC, 2002, Modulation of tRNAAla identity by inorganic pyrophosphatase., Proc Natl Acad Sci U S A, 2002 Apr 30

 [19] Beuning PJ, Nagan MC, Cramer CJ, Musier-Forsyth K, Gelpí JL, Bashford D, 2002, Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair., RNA, 2002 May

 [20] Hou YM, Schimmel P, 1988, A simple structural feature is a major determinant of the identity of a transfer RNA., Nature, 1988 May 12

 [21] McClain WH, Foss K, 1988, Changing the identity of a tRNA by introducing a G-U wobble pair near the 3' acceptor end., Science, 1988 May 6

 [22] McClain WH, Chen YM, Foss K, Schneider J, 1988, Association of transfer RNA acceptor identity with a helical irregularity., Science, 1988 Dec 23

 [23] Hou YM, Schimmel P, 1989, Modeling with in vitro kinetic parameters for the elaboration of transfer RNA identity in vivo., Biochemistry, 1989 Jun 13

 [24] Musier-Forsyth K, Schimmel P, 1992, Functional contacts of a transfer RNA synthetase with 2'-hydroxyl groups in the RNA minor groove., Nature, 1992 Jun 11

 [25] Beuning PJ, Yang F, Schimmel P, Musier-Forsyth K, 1997, Specific atomic groups and RNA helix geometry in acceptor stem recognition by a tRNA synthetase., Proc Natl Acad Sci U S A, 1997 Sep 16

 [26] Chang KY, Varani G, Bhattacharya S, Choi H, McClain WH, 1999, Correlation of deformability at a tRNA recognition site and aminoacylation specificity., Proc Natl Acad Sci U S A, 1999 Oct 12

 [27] Miller WT, Hou YM, Schimmel P, 1991, Mutant aminoacyl-tRNA synthetase that compensates for a mutation in the major identity determinant of its tRNA., Biochemistry, 1991 Mar 12

 [28] Buechter DD, Schimmel P, 1995, Minor groove recognition of the critical acceptor helix base pair by an appended module of a class II tRNA synthetase., Biochemistry, 1995 May 9

 [29] Shi JP, Francklyn C, Hill K, Schimmel P, 1990, A nucleotide that enhances the charging of RNA minihelix sequence variants with alanine., Biochemistry, 1990 Apr 17

 [30] Shi JP, Schimmel P, 1991, Aminoacylation of alanine minihelices. "Discriminator" base modulates transition state of single turnover reaction., J Biol Chem, 1991 Feb 15

 [31] Fischer AE, Beuning PJ, Musier-Forsyth K, 1999, Identification of discriminator base atomic groups that modulate the alanine aminoacylation reaction., J Biol Chem, 1999 Dec 24

 [32] Nagan MC, Beuning P, Musier-Forsyth K, Cramer CJ, 2000, Importance of discriminator base stacking interactions: molecular dynamics analysis of A73 microhelix(Ala) variants., Nucleic Acids Res, 2000 Jul 1

 [33] Park SJ, Miller WT, Schimmel P, 1990, Synthetic peptide model of an essential region of an aminoacyl-tRNA synthetase., Biochemistry, 1990 Oct 2

 [34] Ribas de Pouplana L, Buechter D, Sardesai NY, Schimmel P, 1998, Functional analysis of peptide motif for RNA microhelix binding suggests new family of RNA-binding domains., EMBO J, 1998 Sep 15

 [35] Putney SD, Royal NJ, Neuman de Vegvar H, Herlihy WC, Biemann K, Schimmel P, 1981, Primary structure of a large aminoacyl-tRNA synthetase., Science, 1981 Sep 25

 [36] Jasin M, Regan L, Schimmel P, 1983, Modular arrangement of functional domains along the sequence of an aminoacyl tRNA synthetase., Nature, 1983 Dec 1-7

 [37] Jasin M, Regan L, Schimmel P, 1985, Two mutations in the dispensable part of alanine tRNA synthetase which affect the catalytic activity., J Biol Chem, 1985 Feb 25

 [38] Ho C, Jasin M, Schimmel P, 1985, Amino acid replacements that compensate for a large polypeptide deletion in an enzyme., Science, 1985 Jul 26

 [39] Regan L, Bowie J, Schimmel P, 1987, Polypeptide sequences essential for RNA recognition by an enzyme., Science, 1987 Mar 27

 [40] Lu Y, Hill KA, 1994, 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 Apr 22

 [41] Davis MW, Buechter DD, Schimmel P, 1994, Functional dissection of a predicted class-defining motif in a class II tRNA synthetase of unknown structure., Biochemistry, 1994 Aug 23

 [42] Wu MX, Filley SJ, Xiong J, Lee JJ, Hill KA, 1994, A cysteine in the C-terminal region of alanyl-tRNA synthetase is important for aminoacylation activity., Biochemistry, 1994 Oct 11

 [43] Shi JP, Musier-Forsyth K, Schimmel P, 1994, 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 May 3

 [44] Hill K, Schimmel P, 1989, Evidence that the 3' end of a tRNA binds to a site in the adenylate synthesis domain of an aminoacyl-tRNA synthetase., Biochemistry, 1989 Mar 21

 [45] Filley SJ, Hill KA, 1993, Amino acid substitutions at position 73 in motif 2 of Escherichia coli alanyl-tRNA synthetase., Arch Biochem Biophys, 1993 Nov 15

 [46] Zhang CM, Perona JJ, Ryu K, Francklyn C, Hou YM, 2006, Distinct kinetic mechanisms of the two classes of Aminoacyl-tRNA synthetases., J Mol Biol, 2006 Aug 11

 [47] Barends S, Wower J, Kraal B, 2000, Kinetic parameters for tmRNA binding to alanyl-tRNA synthetase and elongation factor Tu from Escherichia coli., Biochemistry, 2000 Mar 14

 [48] Tsui WC, Fersht AR, 1981, Probing the principles of amino acid selection using the alanyl-tRNA synthetase from Escherichia coli., Nucleic Acids Res, 1981 Sep 25

 [49] Beebe K, Merriman E, Schimmel P, 2003, Structure-specific tRNA determinants for editing a mischarged amino acid., J Biol Chem, 2003 Nov 14

 [50] Guo M, Chong YE, Shapiro R, Beebe K, Yang XL, Schimmel P, 2009, Paradox of mistranslation of serine for alanine caused by AlaRS recognition dilemma., Nature, 2009 Dec 10

 [51] Beebe K, Mock M, Merriman E, Schimmel P, 2008, Distinct domains of tRNA synthetase recognize the same base pair., Nature, 2008 Jan 3

 [52] Pasman Z, Robey-Bond S, Mirando AC, Smith GJ, Lague A, Francklyn CS, 2011, Substrate specificity and catalysis by the editing active site of Alanyl-tRNA synthetase from Escherichia coli., Biochemistry, 2011 Mar 8

 [53] Novoa EM, Vargas-Rodriguez O, Lange S, Goto Y, Suga H, Musier-Forsyth K, Ribas de Pouplana L, 2015, Ancestral AlaX editing enzymes for control of genetic code fidelity are not tRNA-specific., J Biol Chem, 2015 Apr 17

 [54] Pawar KI, Suma K, Seenivasan A, Kuncha SK, Routh SB, Kruparani SP, Sankaranarayanan R, 2017, Role of D-aminoacyl-tRNA deacylase beyond chiral proofreading as a cellular defense against glycine mischarging by AlaRS., Elife, 2017 Mar 31

 [55] Jasin M, Regan L, Schimmel P, 1984, Dispensable pieces of an aminoacyl tRNA synthetase which activate the catalytic site., Cell, 1984 Apr

 [56] Guo M, Chong YE, Beebe K, Shapiro R, Yang XL, Schimmel P, 2009, The C-Ala domain brings together editing and aminoacylation functions on one tRNA., Science, 2009 Aug 7

 [57] Banerjee B, Banerjee R, 2015, Urea Unfolding Study of E. coli Alanyl-tRNA Synthetase and Its Monomeric Variants Proves the Role of C-Terminal Domain in Stability., J Amino Acids, 2015

 [58] Jovanovic M, Lilic M, Janjusevic R, Jovanovic G, Savic DJ, 1999, tRNA synthetase mutants of Escherichia coli K-12 are resistant to the gyrase inhibitor novobiocin., J Bacteriol, 1999 May

 [59] Wittmann HG, Stöffler G, 1974, Altered S5 and S20 ribosomal proteins in revertants of an alanyl-tRNA synthetase mutant of Escherichia coli., Mol Gen Genet, 1974

 [60] Buckel P, Piepersberg W, Böck A, 1976, Suppression of temperature-sensitive aminoacyl-tRNA synthetase mutations by ribosomal mutations: a possible mechanism., Mol Gen Genet, 1976 Nov 24

 [61] Yao P., Poruri K., Martinis SA., Fox PL., 2014, Non-catalytic regulation of gene expression by aminoacyl-tRNA synthetases., Top Curr Chem 344:167-87

 [62] Guo M, Schimmel P, 2012, Structural analyses clarify the complex control of mistranslation by tRNA synthetases., Curr Opin Struct Biol, 2012 Feb

 [63] Reynolds NM, Lazazzera BA, Ibba M, 2010, Cellular mechanisms that control mistranslation., Nat Rev Microbiol, 2010 Dec

 [64] Ataide SF, Ibba M, 2006, Small molecules: big players in the evolution of protein synthesis., ACS Chem Biol, 2006 Jun 20

 [65] Ibba M, Soll D, 2000, Aminoacyl-tRNA synthesis., Annu Rev Biochem, 2000

 [66] Hou YM, Francklyn C, Schimmel P, 1989, Molecular dissection of a transfer RNA and the basis for its identity., Trends Biochem Sci, 1989 Jun

 [67] Miller WT, Schimmel P, 1992, A metal-binding motif implicated in RNA recognition by an aminoacyl-tRNA synthetase and by a retroviral gene product., Mol Microbiol, 1992 May



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