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AlaS DNA-binding transcriptional repressor

Synonyms: AlaS-L-alanine
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]. AlaRS was seen as a homotetramer in solution [3]. Later experiments determined that AlaRS is homodimeric in solution [4] and can exist in an equilibrium between a homodimeric and a homodecameric state, depending on temperature []. The enzyme contains one molecule of zinc per AlaS polypeptide [5]; zinc binds cooperatively and induces a conformational change in AlaRS [].
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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-L-alanine Functional   [APPHINH], [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
ccgggctggtAACTGAAAAGTGGGAATAAGATAAGTTTTCTTGActgggaagta
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    

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

 [HIFS] Human inference of function from sequence

 [IEP] Inferred from expression pattern

 [BPP] Binding of purified proteins

 [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 347(6289):203-6

 [3] 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 256(1):198-204

 [4] 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 50(45):9886-900

 [5] Miller WT., Hill KA., Schimmel P., 1991, Evidence for a "cysteine-histidine box" metal-binding site in an Escherichia coli aminoacyl-tRNA synthetase., Biochemistry 30(28):6970-6

 [6] Putney SD., Royal NJ., Neuman de Vegvar H., Herlihy WC., Biemann K., Schimmel P., 1981, Primary structure of a large aminoacyl-tRNA synthetase., Science 213(4515):1497-501

 [7] Tsui WC., Fersht AR., 1981, Probing the principles of amino acid selection using the alanyl-tRNA synthetase from Escherichia coli., Nucleic Acids Res 9(18):4627-37

 [8] 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 462(7274):808-12

 [9] Beebe K., Mock M., Merriman E., Schimmel P., 2008, Distinct domains of tRNA synthetase recognize the same base pair., Nature 451(7174):90-3

 [10] 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 6



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