Journal of Molecular Biology
Volume 304, Issue 5, 15 December 2000, Pages 847-859
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Regular Article
Modeling the cAMP-induced Allosteric Transition Using the Crystal Structure of CAP-cAMP at 2.1 Å Resolution

https://doi.org/10.1006/jmbi.2000.4231Get rights and content

Abstract

After an allosteric transition produced by the binding of cyclic AMP (cAMP), the Escherichia coli catabolite gene activator protein (CAP) binds DNA specifically and activates transcription. The three-dimensional crystal structure of the CAP-cAMP complex has been refined at 2.1 Å resolution, thus enabling a better evaluation of the structural basis for CAP phenotypes, the interactions of cAMP with CAP and the roles played by water structure. A review of mutational analysis of CAP together with the additional structural information presented here suggests a possible mechanism for the cAMP-induced allostery required for DNA binding and transcriptional activation. We hypothesize that cAMP binding may reorient the coiled-coil C-helices, which provide most of the dimer interface, thereby altering the relative positions of the DNA-binding domains of the CAP dimer. Additionally, cAMP binding may cause a further rearrangement of the DNA-binding and cAMP-binding domains of CAP via a flap consisting of β-strands 4 and 5 which lies over the cAMP.

References (56)

  • S.C. Schultz et al.

    Crystallization of Escherichia coli catabolite gene activator protein with its DNA binding site. The use of modular DNA

    J. Mol. Biol.

    (1990)
  • J.B. Shabb et al.

    Cyclic nucleotide-binding domains in proteins having diverse functions

    J. Biol. Chem.

    (1992)
  • S. Spiro et al.

    FNR and its role in oxygen-regulated gene expression in Escherichia coli

    FEMS Microbiol. Rev.

    (1990)
  • I.T. Weber et al.

    Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 Å resolution

    J. Mol. Biol.

    (1987)
  • I.T. Weber et al.

    Crystal structure of a cyclic AMP-independent mutant of catabolite gene activator protein

    J. Biol. Chem.

    (1987)
  • H. Aiba et al.

    Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein

    Nucl. Acids Res.

    (1982)
  • H. Aiba et al.

    Mutations that alter the allosteric nature of cAMP receptor protein of Escherichia coli

    EMBO J.

    (1985)
  • N. Baichoo et al.

    Mapping cyclic nucleotide-induced conformational changes in cyclicAMP receptor protein by a protein footprinting technique using different chemical proteases

    Protein Sci.

    (1999)
  • A.O. Belduz et al.

    Mutagenesis of the cyclic AMP receptor protein of Escherichia coli: targeting positions 72 and 82 of the cyclic nucleotide binding pocket

    Nucl. Acids Res.

    (1993)
  • A.T. Brunger

    XPLOR Version 3.1 Manual

    (1992)
  • S. Busby et al.

    Positive regulation of gene expression by cyclic AMP and its receptor protein in Escherichia coli

    Microb. Sci.

    (1987)
  • X. Cheng et al.

    Absolute requirement of cyclic nucleotide in the activation of the G141Q mutant cAMP receptor protein from Escherichia coli

    J. Biol. Chem

    (1994)
  • X. Cheng et al.

    Probing the mechanism of CRP activation by site-directed mutagenesis: the role of serine 128 in the allosteric pathway of cAMP receptor protein activation

    Biochemistry

    (1995)
  • K.L. Clark et al.

    Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5

    Nature

    (1993)
  • P. Cossart et al.

    Cloning sequence of the CRP gene of Escherichia coli K 12

    Nucl. Acids Res.

    (1982)
  • T.E. Creighton

    The folded conformation of globular proteins

    Proteins

    (1984)
  • D.M. Crothers et al.

    Transcriptional activation by Escherichia coli CAP protein

    Transcriptional Regulation

    (1992)
  • B. deCrombrugghe et al.

    Cyclic AMP receptor protein: role in transcription activation

    Science

    (1984)
  • Cited by (0)

    Edited by K. Nagai

    f1

    Corresponding author

    f2

    E-mail address of the corresponding author: [email protected]

    f3

    Present addresses: J.M. Passner, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, NY 10029, USA; S.C. Schultz, Math/Science Division, Diné College, Tsaile, Navajo Nation (AZ) 86556, USA.

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