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BirA DNA-binding transcriptional repressor

Synonyms: BirA-biotinyl-5'-adenylate, BirA
Summary:
BirA is a bifunctional protein that exhibits biotin ligase activity and also acts as the DNA binding transcriptional repressor of the biotin operon [1]. The effector of BirA transcriptional repression activity, biotinyl-5'-adenylate (bio-5'-AMP), is also a substrate in the BirA-mediated biotinylation of the biotin carboxyl carrier protein monomer (apoBCCP), and this relationship results in repression of the biotin operon when the abundance of apoBCCP (and therefore the cellular demand for biotin) is reduced [2]. The enzymatic functions include the synthesis of the enzyme-bound biotinyl-5'-adenylate (bio-5'-AMP), and the transfer of the biotin from the adenylate to a lysine residue of the biotin carboxyl carrier protein (BCCP) of the acetyl-CoA-carboxylase. The transfer reaction results in the active form of acetyl-CoA-carboxylase. Alternatively, as a regulator, the enzyme-bound to bio-5'-AMP represses transcription of the biotin biosynthetic operon by binding to the biotin operator sequence [1, 3, 4, 5, 6, 7]. BirA is observed to be predominantly monomeric in solution [1, 8, 9], with some minor multimeric species observed [1].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
BirA Non-Functional   Apo nd nd nd
BirA-biotinyl-5'-adenylate Functional Allosteric Holo nd nd nd
Evolutionary Family: BirA
TFBs length: 40
Sensing class: Using internal synthesized signals
Connectivity class: Local Regulator
Gene name: birA
  Genome position: 4173082-4174047
  Length: 966 bp / 321 aa
Operon name: murB-birA
TU(s) encoding the TF:
Transcription unit        Promoter
murB-birA
 


Regulon       
Regulated gene(s) bioA, bioB, bioC, bioD, bioF
Multifun term(s) of regulated gene(s)
biotin (5)
Regulated operon(s) bioA, bioBFCD
First gene in the operon(s) bioA, bioB
Simple and complex regulons BirA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[BirA,-](2)


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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  BirA-biotinyl-5'-adenylate repressor bioAp Sigma70 11.5 -24.5 bioA
aattcggtgtAGACTTGTAAACCTAAATCTTTTCAATTTGGTTTACAAGTCgattatgaca
809262 809302 [EXP-IMP-SITE-MUTATION] nd
  BirA-biotinyl-5'-adenylate repressor bioBp Sigma70 -20.5 -62.5 bioB, bioF, bioC, bioD
tgtcataatcGACTTGTAAACCAAATTGAAAAGATTTAGGTTTACAAGTCTacaccgaatt
809262 809302 [EXP-IMP-SITE-MUTATION] nd


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




Reference(s)    

 [1] Eisenberg MA, Prakash O, Hsiung SC, 1982, Purification and properties of the biotin repressor. A bifunctional protein., J Biol Chem, 257(24):15167 None

 [2] Beckett D., 1998, Energetic methods to study bifunctional biotin operon repressor., Methods Enzymol 295:424-50

 [3] Buoncristiani MR, Otsuka AJ, 1988, Overproduction and rapid purification of the biotin operon repressor from Escherichia coli., J Biol Chem, 263(2):1013 None

 [4] Cronan JE., 1989, The E. coli bio operon: transcriptional repression by an essential protein modification enzyme., Cell 58(3):427-9

 [5] Wilson KP, Shewchuk LM, Brennan RG, Otsuka AJ, Matthews BW, 1992, Escherichia coli biotin holoenzyme synthetase/bio repressor crystal structure delineates the biotin- and DNA-binding domains., Proc Natl Acad Sci U S A, 89(19):9257 10.1073/pnas.89.19.9257

 [6] Xu Y, Johnson CR, Beckett D, 1996, Thermodynamic analysis of small ligand binding to the Escherichia coli repressor of biotin biosynthesis., Biochemistry, 35(17):5509 10.1021/bi9600658

 [7] Xu Y, Nenortas E, Beckett D, 1995, Evidence for distinct ligand-bound conformational states of the multifunctional Escherichia coli repressor of biotin biosynthesis., Biochemistry, 34(51):16624 10.1021/bi00051a010

 [8] Abbott J, Beckett D, 1993, Cooperative binding of the Escherichia coli repressor of biotin biosynthesis to the biotin operator sequence., Biochemistry, 32(37):9649 10.1021/bi00088a017

 [9] Streaker ED, Beckett D, 1998, Coupling of site-specific DNA binding to protein dimerization in assembly of the biotin repressor-biotin operator complex., Biochemistry, 37(9):3210 10.1021/bi9715019

 [10] Lin KC., Campbell A., Shiuan D., 1991, Binding characteristics of Escherichia coli biotin repressor-operator complex., Biochim Biophys Acta 1090(3):317-25

 [11] Subrahmanyam S, Cronan JE, 1999, Isolation from genomic DNA of sequences binding specific regulatory proteins by the acceleration of protein electrophoretic mobility upon DNA binding., Gene, 226(2):263 10.1016/s0378-1119(98)00548-4

 [12] Streaker ED, Beckett D, 2003, Coupling of protein assembly and DNA binding: biotin repressor dimerization precedes biotin operator binding., J Mol Biol, 325(5):937 10.1016/s0022-2836(02)01308-6

 [13] Weaver LH, Kwon K, Beckett D, Matthews BW, 2001, Competing protein:protein interactions are proposed to control the biological switch of the E coli biotin repressor., Protein Sci, 10(12):2618 10.1110/ps.32701

 [14] Eisenstein E, Beckett D, 1999, Dimerization of the Escherichia coli biotin repressor: corepressor function in protein assembly., Biochemistry, 38(40):13077 10.1021/bi991241q

 [15] Weaver LH, Kwon K, Beckett D, Matthews BW, 2001, Corepressor-induced organization and assembly of the biotin repressor: a model for allosteric activation of a transcriptional regulator., Proc Natl Acad Sci U S A, 98(11):6045 10.1073/pnas.111128198

 [16] Prakash O., Eisenberg MA., 1978, In vitro synthesis and and regulation of the biotin enzymes of Escherichia coli K-12., J Bacteriol 134(3):1002-12

 [17] Brennan RG, Vasu S, Matthews BW, Otsuka AJ, 1989, Crystallization of the bifunctional biotin operon repressor., J Biol Chem, 264(1):5 None

 [18] Streaker ED, Beckett D, 1999, Ligand-linked structural changes in the Escherichia coli biotin repressor: the significance of surface loops for binding and allostery., J Mol Biol, 292(3):619 10.1006/jmbi.1999.3086

 [19] Kwon K, Streaker ED, Ruparelia S, Beckett D, 2000, Multiple disordered loops function in corepressor-induced dimerization of the biotin repressor., J Mol Biol, 304(5):821 10.1006/jmbi.2000.4249

 [20] Kwon K, Streaker ED, Beckett D, 2002, Binding specificity and the ligand dissociation process in the E. coli biotin holoenzyme synthetase., Protein Sci, 11(3):558 10.1110/ps.33502

 [21] Xu Y, Beckett D, 1994, Kinetics of biotinyl-5'-adenylate synthesis catalyzed by the Escherichia coli repressor of biotin biosynthesis and the stability of the enzyme-product complex., Biochemistry, 33(23):7354 10.1021/bi00189a041

 [22] Nenortas E, Beckett D, 1996, Purification and characterization of intact and truncated forms of the Escherichia coli biotin carboxyl carrier subunit of acetyl-CoA carboxylase., J Biol Chem, 271(13):7559 10.1074/jbc.271.13.7559

 [23] Streaker ED, Gupta A, Beckett D, 2002, The biotin repressor: thermodynamic coupling of corepressor binding, protein assembly, and sequence-specific DNA binding., Biochemistry, 41(48):14263 10.1021/bi0203839

 [24] Schatz PJ, 1993, Use of peptide libraries to map the substrate specificity of a peptide-modifying enzyme: a 13 residue consensus peptide specifies biotinylation in Escherichia coli., Biotechnology (N Y), 11(10):1138 10.1038/nbt1093-1138

 [25] Cronan JE, 1990, Biotination of proteins in vivo. A post-translational modification to label, purify, and study proteins., J Biol Chem, 265(18):10327 None

 [26] Beckett D, Kovaleva E, Schatz PJ, 1999, A minimal peptide substrate in biotin holoenzyme synthetase-catalyzed biotinylation., Protein Sci, 8(4):921 10.1110/ps.8.4.921

 [27] Reche PA, Howard MJ, Broadhurst RW, Perham RN, 2000, Heteronuclear NMR studies of the specificity of the post-translational modification of biotinyl domains by biotinyl protein ligase., FEBS Lett, 479(3):93 10.1016/s0014-5793(00)01829-9

 [28] Polyak SW, Chapman-Smith A, Mulhern TD, Cronan JE, Wallace JC, 2001, Mutational analysis of protein substrate presentation in the post-translational attachment of biotin to biotin domains., J Biol Chem, 276(5):3037 10.1074/jbc.M003968200

 [29] Murtif VL, Samols D, 1987, Mutagenesis affecting the carboxyl terminus of the biotinyl subunit of transcarboxylase. Effects on biotination., J Biol Chem, 262(24):11813 None

 [30] Val DL, Chapman-Smith A, Walker ME, Cronan JE, Wallace JC, 1995, Polymorphism of the yeast pyruvate carboxylase 2 gene and protein: effects on protein biotinylation., Biochem J, 312 ( Pt 3)(None):817 10.1042/bj3120817

 [31] He C, Custer G, Wang J, Matysiak S, Beckett D, 2018, Superrepression through Altered Corepressor-Activated Protein:Protein Interactions., Biochemistry, 57(7):1119 10.1021/acs.biochem.7b01122

 [32] Wang J, Samanta R, Custer G, Look C, Matysiak S, Beckett D, 2020, Tuning Allostery through Integration of Disorder to Order with a Residue Network., Biochemistry, 59(6):790 10.1021/acs.biochem.9b01006

 [33] Xu Y, Beckett D, 1996, Evidence for interdomain interaction in the Escherichia coli repressor of biotin biosynthesis from studies of an N-terminal domain deletion mutant., Biochemistry, 35(6):1783 10.1021/bi952269e

 [34] Buoncristiani MR., Howard PK., Otsuka AJ., 1986, DNA-binding and enzymatic domains of the bifunctional biotin operon repressor (BirA) of Escherichia coli., Gene 44(2-3):255-61

 [35] Kwon K, Beckett D, 2000, Function of a conserved sequence motif in biotin holoenzyme synthetases., Protein Sci, 9(8):1530 10.1110/ps.9.8.1530

 [36] Chapman-Smith A, Mulhern TD, Whelan F, Cronan JE, Wallace JC, 2001, The C-terminal domain of biotin protein ligase from E. coli is required for catalytic activity., Protein Sci, 10(12):2608 10.1110/ps.22401

 [37] Saviranta P, Haavisto T, Rappu P, Karp M, Lövgren T, 1998, In vitro enzymatic biotinylation of recombinant fab fragments through a peptide acceptor tail., Bioconjug Chem, 9(6):725 10.1021/bc9800217

 [38] Wu SC, Yeung JC, Hwang PM, Wong SL, 2002, Design, production, and characterization of an engineered biotin ligase (BirA) and its application for affinity purification of staphylokinase produced from Bacillus subtilis via secretion., Protein Expr Purif, 24(3):357 10.1006/prep.2001.1583

 [39] Reche PA., 2000, Lipoylating and biotinylating enzymes contain a homologous catalytic module., Protein Sci 9(10):1922-9

 [40] Duffy S, Tsao KL, Waugh DS, 1998, Site-specific, enzymatic biotinylation of recombinant proteins in Spodoptera frugiperda cells using biotin acceptor peptides., Anal Biochem, 262(2):122 10.1006/abio.1998.2770

 [41] Smith PA, Tripp BC, DiBlasio-Smith EA, Lu Z, LaVallie ER, McCoy JM, 1998, A plasmid expression system for quantitative in vivo biotinylation of thioredoxin fusion proteins in Escherichia coli., Nucleic Acids Res, 26(6):1414 10.1093/nar/26.6.1414

 [42] Parrott MB, Barry MA, 2001, Metabolic biotinylation of secreted and cell surface proteins from mammalian cells., Biochem Biophys Res Commun, 281(4):993 10.1006/bbrc.2001.4437

 [43] Jander G, Cronan JE, Beckwith J, 1996, Biotinylation in vivo as a sensitive indicator of protein secretion and membrane protein insertion., J Bacteriol, 178(11):3049 10.1128/jb.178.11.3049-3058.1996

 [44] Cloutier SM, Couty S, Terskikh A, Marguerat L, Crivelli V, Pugnières M, Mani JC, Leisinger HJ, Mach JP, Deperthes D, 2000, Streptabody, a high avidity molecule made by tetramerization of in vivo biotinylated, phage display-selected scFv fragments on streptavidin., Mol Immunol, 37(17):1067 10.1016/s0161-5890(01)00023-2

 [45] Skowronek K, Kasprzak AA, 2002, A two-plasmid system for independent genetic manipulation of subunits of homodimeric proteins and selective isolation of chimeric dimers., Anal Biochem, 300(2):185 10.1006/abio.2001.5456

 [46] Steinkühler C, Biasiol G, Cerretani M, Di Renzo L, Brunetti M, Ingallinella P, De Francesco R, Altamura S, 2002, A scintillation proximity active site binding assay for the hepatitis C virus serine protease., Anal Biochem, 307(1):99 10.1016/s0003-2697(02)00013-1

 [47] Campbell A., Del Campillo-Campbell A., Chang R., 1972, A mutant of Escherichia coli that requires high concentrations of biotin., Proc Natl Acad Sci U S A 69(3):676-80

 [48] Pai CH., 1972, Mutant of Escherichia coli with derepressed levels of the biotin biosynthetic enzymes., J Bacteriol 112(3):1280-7

 [49] Eisenberg MA., Mee B., Prakash O., Eisenberg MR., 1975, Properties of alpha-dehydrobiotin-resistant mutants of Escherichia coli K-12., J Bacteriol 122(1):66-72

 [50] Howard PK., Shaw J., Otsuka AJ., 1985, Nucleotide sequence of the birA gene encoding the biotin operon repressor and biotin holoenzyme synthetase functions of Escherichia coli., Gene 35(3):321-31

 [51] Barker DF, Campbell AM, 1980, Use of bio-lac fusion strains to study regulation of biotin biosynthesis in Escherichia coli., J Bacteriol, 143(2):789 10.1128/jb.143.2.789-800.1980

 [52] Campbell A., Chang R., Barker D., Ketner G., 1980, Biotin regulatory (bir) mutations of Escherichia coli., J Bacteriol 142(3):1025-8

 [53] Pai CH, 1973, Biotin uptake in biotin regulatory mutant of Escherichia coli., J Bacteriol, 116(1):494 10.1128/jb.116.1.494-496.1973

 [54] Commichau FM, Stülke J, 2008, Trigger enzymes: bifunctional proteins active in metabolism and in controlling gene expression., Mol Microbiol, 67(4):692 10.1111/j.1365-2958.2007.06071.x

 [55] Beckett D, 2007, Biotin sensing: universal influence of biotin status on transcription., Annu Rev Genet, 41(None):443 10.1146/annurev.genet.41.042007.170450

 [56] Chapman-Smith A, Cronan JE, 1999, The enzymatic biotinylation of proteins: a post-translational modification of exceptional specificity., Trends Biochem Sci, 24(9):359 10.1016/s0968-0004(99)01438-3

 [57] Chapman-Smith A, Cronan JE, 1999, In vivo enzymatic protein biotinylation., Biomol Eng, 16(1-4):119 10.1016/s1050-3862(99)00046-7

 [58] Eisenberg MA., 1973, Biotin: biogenesis, transport, and their regulation., Adv Enzymol Relat Areas Mol Biol 38:317-72



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