The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in Gram-positive bacteria

TY - JOUR

T1 - The structure of CodY, a GTP- and isoleucine-responsive regulator of stationary phase and virulence in Gram-positive bacteria

AU - Levdikov, V M

AU - Blagova, E

AU - Joseph, P

AU - Sonenshein, A L

AU - Wilkinson, Tony

PY - 2006/4/21

Y1 - 2006/4/21

N2 - CodY is a global regulator of transcription in Gram-positive bacteria. It represses during growth genes required for adaptation to nutrient limitation, including virulence genes in some human pathogens. CodY activity is regulated by GTP and branched chain amino acids, metabolites whose intracellular concentrations drop as cells enter stationary phase. Although CodY has a highly conserved sequence, it has no significant similarity to proteins of known structure. Here we report crystal structures of two fragments of CodY from Bacillus subtilis that clearly constitute its cofactor and DNA binding domains and reveal that CodY is a chimera of previously observed folding units. The N-terminal cofactor-binding fragment adopts a fold reminiscent of the GAF domains found in cyclic nucleotide phosphodiesterases and adenylate cyclases. It is a dimer stabilized by an intermolecular six alpha-helical bundle that buries an extensive apolar surface rich in residues invariant in CodY orthologues. The branched chain amino acid ligands reside in hydrophobic pockets of each monomer distal to the dimer-forming surface. The structure of the C-terminal DNA binding domain belongs to the winged helix-turn-helix family. The implications of the structure for DNA binding by CodY and its control by cofactor binding are discussed.

AB - CodY is a global regulator of transcription in Gram-positive bacteria. It represses during growth genes required for adaptation to nutrient limitation, including virulence genes in some human pathogens. CodY activity is regulated by GTP and branched chain amino acids, metabolites whose intracellular concentrations drop as cells enter stationary phase. Although CodY has a highly conserved sequence, it has no significant similarity to proteins of known structure. Here we report crystal structures of two fragments of CodY from Bacillus subtilis that clearly constitute its cofactor and DNA binding domains and reveal that CodY is a chimera of previously observed folding units. The N-terminal cofactor-binding fragment adopts a fold reminiscent of the GAF domains found in cyclic nucleotide phosphodiesterases and adenylate cyclases. It is a dimer stabilized by an intermolecular six alpha-helical bundle that buries an extensive apolar surface rich in residues invariant in CodY orthologues. The branched chain amino acid ligands reside in hydrophobic pockets of each monomer distal to the dimer-forming surface. The structure of the C-terminal DNA binding domain belongs to the winged helix-turn-helix family. The implications of the structure for DNA binding by CodY and its control by cofactor binding are discussed.

KW - CHAIN AMINO-ACIDS

KW - BACILLUS-SUBTILIS

KW - TRANSCRIPTIONAL REGULATOR

KW - CRYSTAL-STRUCTURE

KW - LACTOCOCCUS-LACTIS

KW - GLOBAL REGULATOR

KW - MOLECULAR-GRAPHICS

KW - GAF DOMAINS

KW - PROTEIN

KW - DNA

U2 - 10.1074/jbc.M513015200

DO - 10.1074/jbc.M513015200

M3 - Article

SN - 0021-9258

VL - 281

SP - 11366

EP - 11373

JO - Journal of Biological Chemistry

JF - Journal of Biological Chemistry

IS - 16

ER -