RegulonDB RegulonDB 11.1: Gene Form
   

birA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

murB birA coaA rrfB terminator anti-terminator anti-anti-terminator TSS_4698 TSS_4698

Gene      
Name: birA    Texpresso search in the literature
Synonym(s): ECK3965, EG10123, b3973, bioR, dhbB
Genome position(nucleotides): 4173082 --> 4174047
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.38
External database links:  
ASAP:
 ABE-0013001
CGSC:
 952
ECHOBASE:
 EB0121
ECOLIHUB:
 birA
MIM:
 253270
OU-MICROARRAY:
 b3973
STRING:
 511145.b3973
COLOMBOS: birA


Product      
Name: DNA-binding transcriptional repressor/biotin-[acetyl-CoA-carboxylase] ligase BirA
Synonym(s): BioR, BirA, DhbB, biotin-[acetylCoA carboxylase] holoenzyme synthetase and biotin operon repressor
Sequence: Get amino acid sequence Fasta Format
Regulator Family: BirA
Cellular location: cytosol
Molecular weight: 35.312
Isoelectric point: 8.404
Motif(s):
 
Type Positions Sequence Comment
9 -> 58 KLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDVFTVPGKGY
22 -> 41 GEQLGETLGMSRAAINKHIQ UniProt: H-T-H motif.
52 -> 52 T UniProt: Does not affect repressor activity..
57 -> 57 G UniProt: Lack of repressor activity. Does not bind DNA..
58 -> 58 Y UniProt: Lack of repressor activity..

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.3 - cofactors, small molecule carriers --> 1.5.3.1 - biotin
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0017053 - transcription repressor complex
GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0016874 - ligase activity
GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0004077 - biotin-[acetyl-CoA-carboxylase] ligase activity
GO:0009374 - biotin binding
GO:0042803 - protein homodimerization activity
GO:0000976 - transcription cis-regulatory region binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0006464 - cellular protein modification process
GO:0006768 - biotin metabolic process
GO:0009102 - biotin biosynthetic process
GO:0009305 - protein biotinylation
Note(s): Note(s): ...[more].
Evidence: [COMP-HINF-FN-FROM-SEQ] Human inference of function from sequence
[EXP-IPI] Inferred from physical interaction
Reference(s): [1] Barker DF., et al., 1981
[2] Barker DF., et al., 1981
[3] Beckett D. 1998
[4] Buoncristiani MR., et al., 1986
[5] Chapman-Smith A., et al., 1994
[6] Howard PK., et al., 1985
[7] Meydan S., et al., 2019
[8] Otsuka A., et al., 1978
[9] Pai CH., et al., 1975
[10] Prakash O., et al., 1978
[11] Reche PA. 2000
[12] Uchida KM., et al., 1987
External database links:  
ALPHAFOLD:
 P06709
DIP:
 DIP-9224N
DISPROT:
 DP00349
ECOCYC:
 BIOTINLIG-MONOMER
ECOLIWIKI:
 b3973
INTERPRO:
 IPR013196
INTERPRO:
 IPR008988
INTERPRO:
 IPR004409
INTERPRO:
 IPR030855
INTERPRO:
 IPR036388
INTERPRO:
 IPR036390
INTERPRO:
 IPR004143
INTERPRO:
 IPR004408
INTERPRO:
 IPR003142
MODBASE:
 P06709
PDB:
 4WF2
PDB:
 2EWN
PDB:
 1K67
PDB:
 1HXD
PDB:
 1BIA
PDB:
 1BIB
PFAM:
 PF02237
PFAM:
 PF03099
PFAM:
 PF08279
PRIDE:
 P06709
PRODB:
 PRO_000022227
PROSITE:
 PS51733
REFSEQ:
 NP_418404
SMR:
 P06709
UNIPROT:
 P06709


Operon      
Name: murB-birA         
Operon arrangement:
Transcription unit        Promoter
murB-birA


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_4698 4172034 forward nd [RS-EPT-CBR] [13]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Barker DF., Campbell AM., 1981, Genetic and biochemical characterization of the birA gene and its product: evidence for a direct role of biotin holoenzyme synthetase in repression of the biotin operon in Escherichia coli., J Mol Biol 146(4):469-92

 [2] Barker DF., Campbell AM., 1981, The birA gene of Escherichia coli encodes a biotin holoenzyme synthetase., J Mol Biol 146(4):451-67

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

 [4] 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

 [5] Chapman-Smith A., Turner DL., Cronan JE., Morris TW., Wallace JC., 1994, Expression, biotinylation and purification of a biotin-domain peptide from the biotin carboxy carrier protein of Escherichia coli acetyl-CoA carboxylase., Biochem J 302 ( Pt 3):881-7

 [6] 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

 [7] Meydan S., Marks J., Klepacki D., Sharma V., Baranov PV., Firth AE., Margus T., Kefi A., Vazquez-Laslop N., Mankin AS., 2019, Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome., Mol Cell 74(3):481-493.e6

 [8] Otsuka A., Abelson J., 1978, The regulatory region of the biotin operon in Escherichia coli., Nature 276(5689):689-94

 [9] Pai CH., Yau HC., 1975, Chromosomal location of mutations affecting the regualtion of biotin synthesis in Escherichia coli., Can J Microbiol 21(7):1116-20

 [10] 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

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

 [12] Uchida KM., Otsuka AJ., 1987, Isolation and characterization of Escherichia coli birA intragenic suppressors., Mol Gen Genet 210(2):234-40

 [13] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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