A map of the biotin repressor-biotin operator interface: binding of a winged helix-turn-helix protein dimer to a forty base-pair site

Streaker, Emily D.; Beckett, Dorothy

doi:10.1006/jmbi.1998.1733

Cited by 21 publications

(21 citation statements)

References 42 publications

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“…Two holoBirA monomers bind to the 40-bp biotin operator sequence (6). Results of enzymatic and chemical probing of the protein⅐DNA complex are consistent with a structural model in which each DNA binding domain of the holoBirA dimer contacts one of the two 12-bp sequences at the termini of the operator sequence (23). As indicated in Fig.…”

Section: Relationship Of the Structure Of The Bira⅐biotin Complex To supporting

confidence: 80%

“…24) and a number of other protein⅐DNA complexes. Indeed, DNaseI footprinting studies of the complex, as well as circular permutation studies, are consistent with distortion of the DNA as a consequence of holoBirA binding (23). Although the results of circular permutation measurements indicate a net deviation of the Fig.…”

Section: Relationship Of the Structure Of The Bira⅐biotin Complex To supporting

confidence: 67%

“…5). However, the region of contact between the protein and the DNA does not include the more distal parts of the 40-bp site suggested by enzymatic and chemical footprinting (23). Additional contacts within the outermost part of the operator would occur if the DNA were bent around the protein as observed for cAMP-binding protein (CAP; ref.…”

Section: Relationship Of the Structure Of The Bira⅐biotin Complex To mentioning

confidence: 99%

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Corepressor-induced organization and assembly of the biotin repressor: A model for allosteric activation of a transcriptional regulator

Weaver

Kwon

Beckett

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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105

138

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The Escherichia coli biotin repressor binds to the biotin operator to repress transcription of the biotin biosynthetic operon. In this work, a structure determined by x-ray crystallography of a complex of the repressor bound to biotin, which also functions as an activator of DNA binding by the biotin repressor (BirA), is described. In contrast to the monomeric aporepressor, the complex is dimeric with an interface composed in part of an extended ␤-sheet. Model building, coupled with biochemical data, suggests that this is the dimeric form of BirA that binds DNA. Segments of three surface loops that are disordered in the aporepressor structure are located in the interface region of the dimer and exhibit greater order than was observed in the aporepressor structure. The results suggest that the corepressor of BirA causes a disorder-to-order transition that is a prerequisite to repressor dimerization and DNA binding.

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Section: Relationship Of the Structure Of The Bira⅐biotin Complex To supporting

confidence: 80%

Section: Relationship Of the Structure Of The Bira⅐biotin Complex To supporting

confidence: 67%

Section: Relationship Of the Structure Of The Bira⅐biotin Complex To mentioning

confidence: 99%

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Corepressor-induced organization and assembly of the biotin repressor: A model for allosteric activation of a transcriptional regulator

Weaver

Kwon

Beckett

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

105

138

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“…Strain VC233 was transformed with plasmid pVC18 to give strain VC537, which was transduced with the ⌬birA::Km r insertion of strain VC156 to give strain VC618. Strain VC776 was constructed as described in reference 42 by transformation of VC236 with a PCR product encoding the cat::sacB cassette (generated with template CS100 [40,41] and primers VCC44 and VCC49). The insert was confirmed using colony PCR with primers VCA12 and VCA13 and by its birA phenotype on defined medium plates containing 4 M biotin.…”

Section: Methodsmentioning

confidence: 99%

“…1). The dimeric BirA-biotinoyl-adenylate complex represses transcription by binding to the biotin operator (bioO), a 40-bp inverted repeat that overlaps and controls both biotin operon promoters (31,40). In the presence of unmodified acceptor protein, the enzyme-bound biotinoyl-adenylate is attacked by the -amino group of a specific lysine residue of the acceptor protein to give the biotinylated acceptor protein (Fig.…”

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confidence: 99%

Altered Regulation of Escherichia coli Biotin Biosynthesis in BirA Superrepressor Mutant Strains

Chakravartty

Cronan

2011

Journal of Bacteriology

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Transcription of the Escherichia coli biotin (bio) operon is directly regulated by the biotin protein ligase BirA, the enzyme that covalently attaches biotin to its cognate acceptor proteins. Binding of BirA to the bio operator requires dimerization of the protein, which is triggered by BirA-catalyzed synthesis of biotinoyl-adenylate (biotinoyl-5=-AMP), the obligatory intermediate of the ligation reaction. Although several aspects of this regulatory system are well understood, no BirA superrepressor mutant strains had been isolated. Such superrepressor BirA proteins would repress the biotin operon transcription in vivo at biotin concentrations well below those needed for repression by wild-type BirA. We isolated mutant strains having this phenotype by a combined selection-screening approach and resolved multiple mutations to give several birA superrepressor alleles, each having a single mutation, all of which showed repression dominant over that of the wild-type allele. All of these mutant strains repressed bio operon transcription in vivo at biotin concentrations that gave derepression of the wild-type strain and retained sufficient ligation activity for growth when overexpressed. All of the strains except that encoding G154D BirA showed derepression of bio operon transcription upon overproduction of a biotin-accepting protein. In BirA, G154D was a lethal mutation in single copy, and the purified protein was unable to transfer biotin from enzyme-bound biotinoyl-adenylate either to the natural acceptor protein or to a biotin-accepting peptide sequence. Consistent with the transcriptional repression data, each of the purified mutant proteins showed increased affinity for the biotin operator DNA in electrophoretic mobility shift assays. Surprisingly, although most of the mutations were located in the catalytic domain, all of those tested, except G154D BirA, had normal ligase activity. Most of the mutations that gave superrepressor phenotypes altered residues located close to the dimerization interface of BirA. However, two mutations were located at sites well removed from the interface. The properties of the superrepressor mutants strengthen and extend other data indicating that BirA function entails extensive interactions among the three domains of the protein and show that normal ligase activity does not ensure normal DNA binding. In Escherichia coli, the synthesis of the essential enzyme cofactor biotin is regulated at the transcriptional level by an unusual repressor called BirA. BirA is unusual in that it is also an essential metabolic enzyme, the sole biotin protein ligase of this bacterium. Biotin protein ligases are found throughout the three domains of life and catalyze the covalent attachment of biotin to its cognate acceptor proteins that play key roles in central metabolism. The fact that BirA (a protein of 35.3 kDa) is both an enzyme and a transcriptional repressor makes biotin (bio) operon transcription sensitive not only to the intracellular concentration of biotin, but also to the levels of cognate...

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Ligand-linked Structural Changes in the Escherichia coli Biotin Repressor: The Significance of Surface Loops for Binding and Allostery

Streaker

Beckett

1999

Journal of Molecular Biology

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A map of the biotin repressor-biotin operator interface: binding of a winged helix-turn-helix protein dimer to a forty base-pair site

Cited by 21 publications

References 42 publications

Corepressor-induced organization and assembly of the biotin repressor: A model for allosteric activation of a transcriptional regulator

Corepressor-induced organization and assembly of the biotin repressor: A model for allosteric activation of a transcriptional regulator

Altered Regulation of Escherichia coli Biotin Biosynthesis in BirA Superrepressor Mutant Strains

Ligand-linked Structural Changes in the Escherichia coli Biotin Repressor: The Significance of Surface Loops for Binding and Allostery

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