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MetaCyc Protein: BirA-bio-5'-AMP DNA-binding transcriptional repressor

Gene: birA Accession Numbers: EG10123 (MetaCyc), b3973, ECK3965

Synonyms: bioR, dhbB, BirA-bio-5'-AMP

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of BirA-bio-5'-AMP DNA-binding transcriptional repressor = [BirA][biotinyl-5'-adenylate]
         bifunctional biotin-[acetyl-CoA-carboxylase] ligase and transcriptional repressor = BirA (extended summary available)

Summary:
The "biotin repressor," BirA, coordinately represses transcription of the divergent genes that are necessary for the synthesis of biotin [Nath82, Otsuka78]. BirA is a bifunctional protein that possesses both regulatory and enzymatic activities: it acts as the DNA-binding transcriptional repressor of the biotin operon and also exhibits biotin ligase activity [Eisenberg82].

The specific inducer for BirA is biotinyl-5'-adenylate (bio-5'-AMP). In the presence of bio-5'-AMP, BirA binds to 40-nucleotide-long DNA target sites in the bioA/bioBFCD intergenic region to coordinately repress transcription of bioAp and bioBp [Streaker98, Lin91a]. BirA-bio-5'-AMP has been observed to be predominantly monomeric in solution [Eisenberg82, Abbott93, Streaker98], whereas more recent studies indicate that dimerization occurs before DNA binding [Streaker03]. Biotinyl-5'-adenylate [Eisenstein99] and biotin [Weaver01a, Prakash78] stimulate dimerization and DNA binding.

The effector 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 [Beckett98]. This repression is controlled by the rate of the competing protein:protein interaction. The rate of heterodimerization with apoBCCP controls the holoBirA monomer supply, and the equilibrium constant of homodimerization tunes the bioO occupancy and, consequently, transcription initiation at the biotin operon [Adikaram13].

The crystal structure of BirA has been determined by X-ray crystallography to a resolution of 2.3 Å [Wilson92], and that of a BirA-biotin complex [Weaver01a] has been solved by several research groups. Crystallization has been described [Brennan89], and the implications of the structure with respect to the binding of biotin and ATP have been discussed [Wilson92].

The BirA monomer contains three domains: an amino-terminal domain that contains a helix-turn-helix DNA-binding motif; the central domain, which is important for DNA binding and catalysis and contains the binding site for bio-5'-AMP; and the C-terminal domain, the funtion of which has yet to be determinded. Disordered loop structures on the protein surface appear to be involved in binding to biotin, bio-5'-AMP, and/or DNA [Streaker99] and in protein dimerization [Weaver01a]. A model of binding and reaction progression is presented elsewhere [Kwon02].

Locations: cytosol

Map Position: [4,171,105 -> 4,172,070]

Molecular Weight: 35.312 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013001 , CGSC:952 , EchoBASE:EB0121 , EcoGene:EG10123 , OU-Microarray:b3973 , PortEco:birA , RegulonDB:EG10123

Relationship Links: PDB:Structure:1HXD , Pfam:IN-FAMILY:PF03099

Gene-Reaction Schematic: ?

GO Terms:

Cellular Component: GO:0005829 - cytosol

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks cofactors, small molecule carriers biotin
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor

DNA binding site length: 40 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: GACTTGTAAACCtAAaTcttttcAaTTtGGTTTACAAGTC

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Component enzyme of BirA-bio-5'-AMP DNA-binding transcriptional repressor : bifunctional biotin-[acetyl-CoA-carboxylase] ligase and transcriptional repressor

Synonyms: BirA, BioR, DhbB, biotin-[acetylCoA carboxylase] holoenzyme synthetase and biotin operon repressor

Gene: birA Accession Numbers: EG10123 (MetaCyc), b3973, ECK3965

Locations: cytosol

Sequence Length: 321 AAs

Molecular Weight: 35.312 kD (from nucleotide sequence)

pI: 8.05, 8.21

GO Terms:

Biological Process: GO:0009102 - biotin biosynthetic process Inferred from experiment [Barker81]
GO:0009305 - protein biotinylation Inferred from experiment [Roux12]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0006464 - cellular protein modification process Inferred by computational analysis [GOA01]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, Barker81]
GO:0004077 - biotin-[acetyl-CoA-carboxylase] ligase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Barker81a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related Transcription related
metabolism biosynthesis of building blocks cofactors, small molecule carriers biotin
regulation genetic unit regulated operon
regulation type of regulation transcriptional level repressor

Unification Links: DIP:DIP-9224N , DisProt:DP00349 , EcoliWiki:b3973 , Mint:MINT-1254106 , ModBase:P06709 , PR:PRO_000022227 , Protein Model Portal:P06709 , RefSeq:NP_418404 , SMR:P06709 , String:511145.b3973 , UniProt:P06709

Relationship Links: InterPro:IN-FAMILY:IPR003142 , InterPro:IN-FAMILY:IPR004143 , InterPro:IN-FAMILY:IPR004408 , InterPro:IN-FAMILY:IPR004409 , InterPro:IN-FAMILY:IPR008988 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR013196 , Panther:IN-FAMILY:PTHR12835 , PDB:Structure:1BIA , PDB:Structure:1BIB , PDB:Structure:1HXD , PDB:Structure:1K67 , PDB:Structure:2EWN , Pfam:IN-FAMILY:PF02237 , Pfam:IN-FAMILY:PF03099 , Pfam:IN-FAMILY:PF08279

Catalyzes:
a [biotin-carboxyl-carrier protein monomer] + biotin + ATP → AMP + a biotinylated [BCCP monomer] + diphosphate

Summary:
BirA is a bifunctional protein that exhibits biotin ligase activity and also acts as the DNA binding transcriptional repressor of the biotin operon [Eisenberg82]. 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 [Beckett98].

BirA is observed to be predominantly monomeric in solution [Eisenberg82, Abbott93, Streaker98], with some minor multimeric species observed [Eisenberg82]. BirA binds as a dimer to its 40 bp DNA site, the biotin operator [Lin91a]. An additional, low-affinity BirA DNA binding site has been identified [Subrahmanyam99]. Initial models suggested that monomeric BirA-bio-5'-AMP shows cooperative binding to its DNA site [Abbott93], whereas more recent studies indicate that dimerization occurs before DNA binding [Streaker03]. BirA-BCCP binding may preclude dimerization and therefore DNA binding and repressor activity [Weaver01]. Biotinyl-5'-adenylate (bio-5'-AMP, the physiological effector) [Eisenstein99] and biotin [Weaver01a, Prakash78] stimulate dimerization and DNA binding.

Crystal structures at 2.3 angstrom resolution [Wilson92] and of a BirA-biotin complex [Weaver01a] are presented. Crystallization has been described [Brennan89]. The implications of the structure with respect to the binding of biotin and ATP are discussed [Wilson92]. ApoBirA, the BirA-bio-5'-AMP complex, and the BirA-biotin complex have distinct structural characteristics [Xu95e, Streaker99]. DNA binding affects the structure of the C terminus as well as the structure of the N terminus [Streaker99]. Disordered loop structures on the protein surface appear to be involved in binding to biotin, bio-5'-AMP, and/or DNA [Streaker99] and in protein dimerization [Kwon00a, Weaver01a]. A model of binding and reaction progression is presented [Kwon02].

The enzymatic reaction of bio-5'-AMP formation has been kinetically characterized [Xu94b] and the kinetics of biotinylation of biotin carboxyl carrier protein monomer have been determined [Nenortas96]. The thermodynamics of association between BirA and biotin and between BirA and bio-5'-AMP have been characterized [Xu96a, Kwon02], as well as the thermodynamics of dimerization and DNA binding by BirA, the BirA-biotin complex, and the BirA-bio-5'-AMP complex [Streaker02]. Substrate characteristics have been examined [Schatz93, Cronan90, Beckett99, Reche00, Polyak01, Murtif87, Val95].

Some birA mutations cause heat sensitivity [Howard85]. Mutants also show defects in transcriptional repression at the biotin operon promoter [Barker80] and an increased requirement for biotin [Campbell80]. Mutants exhibit resistance to α-dehydrobiotin, defects in repression of the production of the enzymes of biotin synthesis, and increased secretion of biotin vitamers [Eisenburg75]. Deletion of the N-terminal DNA binding domain eliminates DNA binding activity and reduces binding to biotin and bio-5'-AMP, but does not affect the production of bio-5'-AMP or the BCCP biotinylation activity [Xu96b]. The DNA binding region is distinct from the regions in which mutations lead to heat sensitivity [Buoncristiani86]. G115S, R118G, and R119W mutations cause defects in binding to biotin and bio-5'-AMP [Kwon00b]. Mutations in the region that binds bio-5'-AMP also cause defects in dimerization and DNA binding [Kwon00a]. An R317E mutation affects binding to ATP, and a K277E mutation affects substrate recognition [ChapmanSmith01].

BirA overproduction and purification is described [Buoncristiani88]. BirA fusion proteins with affinity tags have been purified [Saviranta98, Wu02].

Structural similarity between lipoylating and biotinylating enzymes, and implications with respect to the catalytic site, are discussed [Reche00a].

BirA has been used as a reagent for biotinylation of exogenous proteins [Duffy98, Smith98a, Parrott01, Jander96, Cloutier00, Skowronek02, Steinkuhler02, Cronan90].

Reviews: [Commichau08, Beckett07, ChapmanSmith99a, ChapmanSmith99b, Cronan89]

Citations: [Barker81, Barker81a, Uchida87, Pai75, ChapmanSmith94, Campbell72, Pai73]

History:
10/20/97 Gene b3973 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10123; confirmed by SwissProt match.


References

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Adikaram13: Adikaram PR, Beckett D (2013). "Protein:protein interactions in control of a transcriptional switch." J Mol Biol 425(22);4584-94. PMID: 23896299

Barker80: Barker DF, Campbell AM (1980). "Use of bio-lac fusion strains to study regulation of biotin biosynthesis in Escherichia coli." J Bacteriol 143(2);789-800. PMID: 6782078

Barker81: 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. PMID: 6456358

Barker81a: Barker DF, Campbell AM (1981). "The birA gene of Escherichia coli encodes a biotin holoenzyme synthetase." J Mol Biol 146(4);451-67. PMID: 7024555

Beckett07: Beckett D (2007). "Biotin Sensing: Universal Influence of Biotin Status on Transcription." Annu Rev Genet 41:443-64. PMID: 17669049

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Brennan89: Brennan RG, Vasu S, Matthews BW, Otsuka AJ (1989). "Crystallization of the bifunctional biotin operon repressor." J Biol Chem 264(1);5. PMID: 2642476

Buoncristiani86: 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. PMID: 3536662

Buoncristiani88: Buoncristiani MR, Otsuka AJ (1988). "Overproduction and rapid purification of the biotin operon repressor from Escherichia coli." J Biol Chem 263(2);1013-6. PMID: 3275654

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Eisenburg75: Eisenburg MA, Mee B, Prakash O, Eisenburg MR (1975). "Properties of alpha-dehydrobiotin-resistant mutants of Escherichia coli K-12." J Bacteriol 122(1);66-72. PMID: 1091631

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Howard85: 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. PMID: 3899863

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Kwon00b: Kwon K, Beckett D (2000). "Function of a conserved sequence motif in biotin holoenzyme synthetases." Protein Sci 9(8);1530-9. PMID: 10975574

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Murtif87: Murtif VL, Samols D (1987). "Mutagenesis affecting the carboxyl terminus of the biotinyl subunit of transcarboxylase. Effects on biotination." J Biol Chem 262(24);11813-6. PMID: 3040718

Nath82: Nath SK, Guha A (1982). "Abortive termination of bioBFCD RNA synthesized in vitro from the bioABFCD operon of Escherichia coli K-12." Proc Natl Acad Sci U S A 79(6);1786-90. PMID: 6177001

Nenortas96: 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);7559-67. PMID: 8631788

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Pai73: Pai CH (1973). "Biotin uptake in biotin regulatory mutant of Escherichia coli." J Bacteriol 116(1);494-6. PMID: 4583224

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Parrott01: Parrott MB, Barry MA (2001). "Metabolic biotinylation of secreted and cell surface proteins from mammalian cells." Biochem Biophys Res Commun 281(4);993-1000. PMID: 11237761

Polyak01: 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);3037-45. PMID: 11042165

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Reche00: 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);93-8. PMID: 10981714

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Weaver01a: 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);6045-50. PMID: 11353844

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Xu95e: 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);16624-31. PMID: 8527435

Xu96a: Xu Y, Johnson CR, Beckett D (1996). "Thermodynamic analysis of small ligand binding to the Escherichia coli repressor of biotin biosynthesis." Biochemistry 35(17);5509-17. PMID: 8611542

Xu96b: 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);1783-92. PMID: 8639659


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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