Structural basis for cAMP-mediated allosteric control of the catabolite activator protein

The cAMP-mediated allosteric transition in the catabolite activator protein (CAP; also known as the cAMP receptor protein, CRP) is a textbook example of modulation of DNA-binding activity by small-molecule binding. Here we report the structure of CAP in the absence of cAMP, which, together with structures of CAP in the presence of cAMP, defines atomic details of the cAMP-mediated allosteric transition. The structural changes, and their relationship to cAMP binding and DNA binding, are remarkably clear and simple. Binding of cAMP results in a coil-to-helix transition that extends the coiled-coil dimerization interface of CAP by 3 turns of helix and concomitantly causes rotation, by ≈60°, and translation, by ≈7 Å, of the DNA-binding domains (DBDs) of CAP, positioning the recognition helices in the DBDs in the correct orientation to interact with DNA. The allosteric transition is stabilized further by expulsion of an aromatic residue from the cAMP-binding pocket upon cAMP binding. The results define the structural mechanisms that underlie allosteric control of this prototypic transcriptional regulatory factor and provide an illustrative example of how effector-mediated structural changes can control the activity of regulatory proteins.

[1]  H. Won,et al.  Stoichiometry and Structural Effect of the Cyclic Nucleotide Binding to Cyclic AMP Receptor Protein* , 2002, The Journal of Biological Chemistry.

[2]  Gottfried Otting,et al.  Alignment of Biological Macromolecules in Novel Nonionic Liquid Crystalline Media for NMR Experiments , 2000 .

[3]  T. Steitz,et al.  Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees , 1991, Science.

[4]  R. Ebright,et al.  Analogs of cyclic AMP that elicit the biochemically defined conformational change in catabolite gene activator protein (CAP) but do not stimulate binding to DNA. , 1985, Journal of molecular biology.

[5]  Y. Kyōgoku,et al.  Structural understanding of the allosteric conformational change of cyclic AMP receptor protein by cyclic AMP binding. , 2000, Biochemistry.

[6]  Helen M. Berman,et al.  Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface. , 1997, Journal of molecular biology.

[7]  J. Lee,et al.  Interplay between site-specific mutations and cyclic nucleotides in modulating DNA recognition by Escherichia coli cyclic AMP receptor protein. , 2004, Biochemistry.

[8]  Rich Olson,et al.  Structural basis for modulation and agonist specificity of HCN pacemaker channels , 2003, Nature.

[9]  Nguyen-Huu Xuong,et al.  Crystal Structure of a Complex Between the Catalytic and Regulatory (RIα) Subunits of PKA , 2005, Science.

[10]  G. Wagner,et al.  Utilization of site-directed spin labeling and high-resolution heteronuclear nuclear magnetic resonance for global fold determination of large proteins with limited nuclear overhauser effect data. , 2000, Biochemistry.

[11]  Ad Bax,et al.  Weak alignment NMR: a hawk-eyed view of biomolecular structure. , 2005, Current opinion in structural biology.

[12]  D. Swigon,et al.  Catabolite activator protein: DNA binding and transcription activation. , 2004, Current opinion in structural biology.

[13]  T. Poulos,et al.  Structure-based hypothesis on the activation of the CO-sensing transcription factor CooA. , 2007, Acta crystallographica. Section D, Biological crystallography.

[14]  Susan S. Taylor,et al.  The cAMP binding domain: an ancient signaling module. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[15]  G. Roberts,et al.  Two-State Allosteric Modeling Suggests Protein Equilibrium as an Integral Component for Cyclic AMP (cAMP) Specificity in the cAMP Receptor Protein of Escherichia coli , 2008, Journal of bacteriology.

[16]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[17]  A. Bax,et al.  Protein backbone angle restraints from searching a database for chemical shift and sequence homology , 1999, Journal of biomolecular NMR.

[18]  R. Kerby,et al.  Study of Highly Constitutively Active Mutants Suggests How cAMP Activates cAMP Receptor Protein* , 2006, Journal of Biological Chemistry.

[19]  R. Ebright,et al.  Dynamically driven protein allostery , 2006, Nature Structural &Molecular Biology.

[20]  L. Kay,et al.  Solution NMR of supramolecular complexes: providing new insights into function , 2007, Nature Methods.

[21]  D. J. Schuller,et al.  Structure of the CO sensing transcription activator CooA , 2000, Nature Structural Biology.

[22]  R. Isaacson,et al.  A new labeling method for methyl transverse relaxation-optimized spectroscopy NMR spectra of alanine residues. , 2007, Journal of the American Chemical Society.

[23]  Helen M. Berman,et al.  Structure of the CAP-DNA Complex at 2.5 Å Resolution: A Complete Picture of the Protein-DNA Interface , 1996 .

[24]  A M Gronenborn,et al.  A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information. , 1998, Journal of magnetic resonance.

[25]  Susan S. Taylor,et al.  Evolution of allostery in the cyclic nucleotide binding module , 2007, Genome Biology.

[26]  S. Adhya,et al.  Sites of allosteric shift in the structure of the cyclic AMP receptor protein , 1985, Cell.

[27]  Wing-Yiu Choy,et al.  Solution NMR-derived global fold of a monomeric 82-kDa enzyme. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[28]  A. Keating,et al.  Structural specificity in coiled-coil interactions. , 2008, Current opinion in structural biology.

[29]  G. Clore,et al.  Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR , 2007, Nature.

[30]  Wolf-Dieter Schubert,et al.  The mutation G145S in PrfA, a key virulence regulator of Listeria monocytogenes, increases DNA‐binding affinity by stabilizing the HTH motif , 2005, Molecular microbiology.

[31]  J G Harman,et al.  Allosteric regulation of the cAMP receptor protein. , 2001, Biochimica et biophysica acta.

[32]  S. Adhya,et al.  Allosteric changes in the cAMP receptor protein of Escherichia coli: hinge reorientation. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[33]  T. Steitz,et al.  Modeling the cAMP-induced allosteric transition using the crystal structure of CAP-cAMP at 2.1 A resolution. , 2000, Journal of molecular biology.

[34]  Heidi J Sofia,et al.  Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs. , 2003, FEMS microbiology reviews.

[35]  Gary Parkinson,et al.  Structural Basis of Transcription Activation: The CAP-αCTD-DNA Complex , 2002, Science.

[36]  T. Steitz,et al.  Structure of catabolite gene activator protein at 2.9 Ã resolution suggests binding to left handed B-DNA , 1981 .

[37]  A. Gunasekera,et al.  Derivatives of CAP having no solvent-accessible cysteine residues, or having a unique solvent-accessible cysteine residue at amino acid 2 of the helix-turn-helix motif. , 1991, Journal of biomolecular structure & dynamics.

[38]  S. Karamanou,et al.  Structural Basis for Signal-Sequence Recognition by the Translocase Motor SecA as Determined by NMR , 2007, Cell.

[39]  H. Smidt,et al.  Molecular basis of halorespiration control by CprK, a CRP-FNR type transcriptional regulator , 2008, Molecular microbiology.

[40]  M. Brunori,et al.  NO sensing in Pseudomonas aeruginosa: structure of the transcriptional regulator DNR. , 2008, Journal of molecular biology.

[41]  A. Wittinghofer,et al.  Structure and regulation of the cAMP-binding domains of Epac2 , 2003, Nature Structural Biology.

[42]  Z. Wasylewski,et al.  Fluorescence study ofEscherichia coli cyclic AMP receptor protein , 1995, Journal of protein chemistry.

[43]  R. Birge,et al.  Proline cis-trans isomerization controls autoinhibition of a signaling protein. , 2007, Molecular cell.

[44]  J. Collado-Vides,et al.  Identifying global regulators in transcriptional regulatory networks in bacteria. , 2003, Current opinion in microbiology.