Home LiteratureArticle Details
PMID: 6390433 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Molecular basis of DNA sequence recognition by the catabolite gene activator protein: detailed inferences from three mutations that alter DNA sequence specificity.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 81 ·No. 23 ·1984-12-00 ·Pages 7274-8

Ebright RH, Cossart P, Gicquel-Sanzey B, Beckwith J

Abstract

Previously, we reported that substitution of Glu-181 of the catabolite gene activator protein (CAP) by lysine, leucine, or valine results in a protein that has specificity for A X T base pairs at positions 7 and 16 of the DNA recognition site, rather than G X C base pairs as is the case with the wild-type CAP. In this paper, we deduce from these genetic data both (i) the specific chemical interactions by which amino acid side chains at position 181 interact with base pairs 7 and 16 and (ii) the precise alignment between the structures of the CAP and DNA in the intermolecular CAP-DNA complex. Our analysis supports the idea that the two symmetry-related F alpha-helices of the CAP dimer interact with successive major grooves of right-handed B-type DNA [Pabo, C. & Lewis, M. (1982) Nature (London) 298, 443-447; and Steitz, T., Weber, I. & Matthew, J. (1983) Cold Spring Harbor Symp. Quant. Biol. 47, 419-426].

MeSH Terms
Base Composition Base Sequence DNA, Bacterial/genetics Escherichia coli/genetics Genes Genes, Bacterial Hydrogen Bonding Models, Molecular Mutation Nucleic Acid Conformation Protein Binding Protein Conformation Receptors, Cyclic AMP/genetics
Chemicals
DNA, Bacterial Receptors, Cyclic AMP
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Ebright R H
Cossart P
Gicquel-Sanzey B
Beckwith J
References (35)
35 references, click to expand
  1. Comparison of the binding sites for the Escherichia coli cAMP receptor protein at the lactose and galactose promoters.
    EMBO J. 1983;2(2):217-22 PMID: 11894929
  2. Evidence for two sites in the lac promoter region.
    J Mol Biol. 1972 Aug 14;69(1):155-60 PMID: 4341750
  3. Sequence-specific recognition of double helical nucleic acids by proteins.
    Proc Natl Acad Sci U S A. 1976 Mar;73(3):804-8 PMID: 1062791
  4. Nucleotide sequence changes produced by mutations in the lac promoter of Escherichia coli.
    J Mol Biol. 1977 Mar 25;111(1):65-75 PMID: 323498
  5. Production and properties of the alpha core derived from the cyclic adenosine monophosphate receptor protein of Escherichia coli.
    Biochemistry. 1978 Jun 27;17(13):2469-73 PMID: 209817
  6. Interaction of the cAMP receptor protein with the lac promoter.
    Nucleic Acids Res. 1980 Feb 25;8(4):759-66 PMID: 6253923
  7. Structure of catabolite gene activator protein at 2.9 A resolution suggests binding to left-handed B-DNA.
    Nature. 1981 Apr 30;290(5809):744-9 PMID: 6261152
  8. Structure of the cro repressor from bacteriophage lambda and its interaction with DNA.
    Nature. 1981 Apr 30;290(5809):754-8 PMID: 6452580
  9. Mechanism for transcriptional action of cyclic AMP in Escherichia coli: entry into DNA to disrupt DNA secondary structure.
    Proc Natl Acad Sci U S A. 1981 Jul;78(7):4011-5 PMID: 6270652
  10. Is DNA unwound by the cyclic AMP receptor protein?
    Nucleic Acids Res. 1982 Jan 22;10(2):473-85 PMID: 6278415
  11. The N-terminal arms of lambda repressor wrap around the operator DNA.
    Nature. 1982 Jul 29;298(5873):441-3 PMID: 7088189
  12. The operator-binding domain of lambda repressor: structure and DNA recognition.
    Nature. 1982 Jul 29;298(5873):443-7 PMID: 7088190
  13. Homology among DNA-binding proteins suggests use of a conserved super-secondary structure.
    Nature. 1982 Jul 29;298(5873):447-51 PMID: 6896364
  14. Structural similarity in the DNA-binding domains of catabolite gene activator and cro repressor proteins.
    Proc Natl Acad Sci U S A. 1982 May;79(10):3097-100 PMID: 6212926
  15. Structure of catabolite gene activator protein at 2.9-A resolution. Incorporation of amino acid sequence and interactions with cyclic AMP.
    J Biol Chem. 1982 Aug 25;257(16):9518-24 PMID: 6286624
  16. The molecular basis of DNA-protein recognition inferred from the structure of cro repressor.
    Nature. 1982 Aug 19;298(5876):718-23 PMID: 6213863
  17. Proton nuclear magnetic resonance studies on cyclic nucleotide binding to the Escherichia coli adenosine cyclic 3',5'-phosphate receptor protein.
    Biochemistry. 1982 Aug 17;21(17):4040-8 PMID: 6289868
  18. Determination of the conformations of cyclic nucleotides bound to the N-terminal core of the cyclic AMP receptor protein of Escherichia coli by 1H-NMR.
    FEBS Lett. 1982 Aug 23;145(2):197-202 PMID: 6290269
  19. Two helix DNA binding motif of CAP found in lac repressor and gal repressor.
    Nucleic Acids Res. 1982 Aug 25;10(16):5085-102 PMID: 6897114
  20. A model for catabolite activator protein binding to supercoiled DNA.
    Proc Natl Acad Sci U S A. 1982 Sep;79(17):5263-7 PMID: 6752942
  21. Proposed alpha-helical super-secondary structure associated with protein-dna recognition.
    J Mol Biol. 1982 Aug 25;159(4):745-51 PMID: 6897265
  22. Repressor structure and the mechanism of positive control.
    Cell. 1983 Feb;32(2):319-25 PMID: 6218886
  23. Mutations in lambda repressor's amino-terminal domain: implications for protein stability and DNA binding.
    Proc Natl Acad Sci U S A. 1983 May;80(9):2676-80 PMID: 6221342
  24. CAP binding to B and Z forms of DNA.
    Nucleic Acids Res. 1983 Apr 25;11(8):2479-94 PMID: 6344018
  25. Chemical synthesis and biological studies on mutated gene-control regions.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:411-8 PMID: 6345060
  26. Catabolite gene activator protein: structure, homology with other proteins, and cyclic AMP and DNA binding.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:419-26 PMID: 6305560
  27. Structure of the operator-binding domain of bacteriophage lambda repressor: implications for DNA recognition and gene regulation.
    Cold Spring Harb Symp Quant Biol. 1983;47 Pt 1:435-40 PMID: 6305562
  28. Specific DNA binding of the cyclic AMP receptor protein to a synthetic oligodeoxyribonucleotide. A circular dichroism study.
    FEBS Lett. 1983 Aug 8;159(1-2):102-6 PMID: 6307748
  29. DNA-binding proteins.
    Science. 1983 Sep 9;221(4615):1020-6 PMID: 6308768
  30. Comparison of the structures of cro and lambda repressor proteins from bacteriophage lambda.
    J Mol Biol. 1983 Sep 25;169(3):757-69 PMID: 6226802
  31. Cyclic AMP receptor protein: role in transcription activation.
    Science. 1984 May 25;224(4651):831-8 PMID: 6372090
  32. Model of specific complex between catabolite gene activator protein and B-DNA suggested by electrostatic complementarity.
    Proc Natl Acad Sci U S A. 1984 Jul;81(13):3973-7 PMID: 6377305
  33. Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli.
    Nature. 1984 Sep 20-26;311(5983):232-5 PMID: 6090927
  34. Systematic analysis of possible hydrogen bonds between amino acid side chains and B-form DNA.
    J Biomol Struct Dyn. 1983 Dec;1(4):1039-49 PMID: 6400903
  35. On the different binding affinities of CRP at the lac, gal and malT promoter regions.
    Nucleic Acids Res. 1983 Nov 25;11(22):7833-52 PMID: 6316274
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.81.23.7274
Published
1984-12-00
Pages
7274-8
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC392128
Subset
IM
Grants
NIGMS NIH HHS · GM13017 · United States
NCRR NIH HHS · RR-01032 · United States
External Links
PubMed source DOI: 10.1073/pnas.81.23.7274 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: [email protected]

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2