DNA-sequence Recognition by CAP: Role of the Adenine N6 Atom of Base Pair 6 of the DNA Site

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1990 Dec 11

PMID 2175880

Citations 2

Authors

A Gunasekera

Y W Ebright

R H Ebright

Affiliations

Soon will be listed here.

Abstract

Two similar, but not identical, models have been proposed for the amino acid-base pair contacts in the CAP-DNA complex ('Model I,' Weber, I. and Steitz, T., Proc. Natl. Acad. Sci. USA, 81, 3973-3977, 1984; 'Model II,' Ebright, et al., Proc. Natl. Acad. Sci. USA, 81, 7274-7278, 1984). One difference between the two models involves Glu181 of CAP. Model I predicts that Glu181 of CAP makes two specificity determining contacts: one H-bond with the cytosine N4 atom of G:C at base pair 7 of the DNA half site, and one H-bond with the adenine N6 atom of T:A at base pair 6 of the DNA half site. In contrast, Model II predicts that Glu181 makes only one specificity determining contact: one H-bond with the cytosine N4 atom of G:C at base pair 7 of the DNA half site. In the present work, we show that replacement of T:A at base pair 6 of the DNA half site by T:N6-methyl-adenine has no, or almost no, effect on the binding of CAP. We conclude, contrary to Model I, that Glu181 of CAP makes no contact with the adenine N6 atom of base pair 6 of the DNA half site.

Citing Articles

Escherichia coli cyclic AMP receptor protein mutants provide evidence for ligand contacts important in activation.

Moore J, Kantorow M, Vanderzwaag D, McKenney K J Bacteriol. 1992; 174(24):8030-5.

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Cloning and expression of the genes for xylose isomerase and xylulokinase from Klebsiella pneumoniae 1033 in Escherichia coli K12.

Feldmann S, Sahm H, Sprenger G Mol Gen Genet. 1992; 234(2):201-10.

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References

Pastan I, Adhya S . Cyclic adenosine 5'-monophosphate in Escherichia coli. Bacteriol Rev. 1976; 40(3):527-51. PMC: 413971. DOI: 10.1128/br.40.3.527-551.1976. View

Zhang X, Ebright R . Identification of a contact between arginine-180 of the catabolite gene activator protein (CAP) and base pair 5 of the DNA site in the CAP-DNA complex. Proc Natl Acad Sci U S A. 1990; 87(12):4717-21. PMC: 54188. DOI: 10.1073/pnas.87.12.4717. View

Eilen E, Pampeno C, Krakow J . Production and properties of the alpha core derived from the cyclic adenosine monophosphate receptor protein of Escherichia coli. Biochemistry. 1978; 17(13):2469-73. DOI: 10.1021/bi00606a001. View

Takeda Y, Ohlendorf D, Anderson W, Matthews B . DNA-binding proteins. Science. 1983; 221(4615):1020-6. DOI: 10.1126/science.6308768. View

de Crombrugghe B, Busby S, Buc H . Cyclic AMP receptor protein: role in transcription activation. Science. 1984; 224(4651):831-8. DOI: 10.1126/science.6372090. View

Weber I, Steitz T . Model of specific complex between catabolite gene activator protein and B-DNA suggested by electrostatic complementarity. Proc Natl Acad Sci U S A. 1984; 81(13):3973-7. PMC: 345350. DOI: 10.1073/pnas.81.13.3973. View

Pabo C, Sauer R . Protein-DNA recognition. Annu Rev Biochem. 1984; 53:293-321. DOI: 10.1146/annurev.bi.53.070184.001453. View

Ebright R, Cossart P, Beckwith J . Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli. Nature. 1984; 311(5983):232-5. DOI: 10.1038/311232a0. View

Ebright R, Cossart P, Beckwith J . Molecular basis of DNA sequence recognition by the catabolite gene activator protein: detailed inferences from three mutations that alter DNA sequence specificity. Proc Natl Acad Sci U S A. 1984; 81(23):7274-8. PMC: 392128. DOI: 10.1073/pnas.81.23.7274. View

10.

Fersht A, Shi J, Lowe D, Wilkinson A, Blow D, Brick P . Hydrogen bonding and biological specificity analysed by protein engineering. Nature. 1985; 314(6008):235-8. DOI: 10.1038/314235a0. View

11.

Quignard E, Fazakerley G, Teoule R, Guy A, GUSCHLBAUER W . Consequences of methylation on the amino group of adenine. A proton two-dimensional NMR study of d(GGATATCC) and d(GGm6ATATCC). Eur J Biochem. 1985; 152(1):99-105. DOI: 10.1111/j.1432-1033.1985.tb09168.x. View

12.

Fazakerley G, Teoule R, Guy A, Fritzsche H, GUSCHLBAUER W . NMR studies on oligodeoxyribonucleotides containing the dam methylation site GATC. Comparison between d(GGATCC) and d(GGm6ATCC). Biochemistry. 1985; 24(17):4540-8. DOI: 10.1021/bi00338a009. View

13.

Brennan C, Van Cleve M, GUMPORT R . The effects of base analogue substitutions on the cleavage by the EcoRI restriction endonuclease of octadeoxyribonucleotides containing modified EcoRI recognition sequences. J Biol Chem. 1986; 261(16):7270-8. View

14.

Rinkel L, van der Marel G, VAN Boom J, Altona C . Influence of N6-methylation of residue A(5) on the conformational behaviour of d(C-C-G-A-A-T-T-C-G-G) in solution studied by 1H-NMR spectroscopy. 1. The duplex form. Eur J Biochem. 1987; 163(2):275-86. DOI: 10.1111/j.1432-1033.1987.tb10798.x. View

15.

Ebright R, Kolb A, Buc H, Kunkel T, Krakow J, Beckwith J . Role of glutamic acid-181 in DNA-sequence recognition by the catabolite gene activator protein (CAP) of Escherichia coli: altered DNA-sequence-recognition properties of [Val181]CAP and [Leu181]CAP. Proc Natl Acad Sci U S A. 1987; 84(17):6083-7. PMC: 299012. DOI: 10.1073/pnas.84.17.6083. View

16.

Weber I, Steitz T . Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 A resolution. J Mol Biol. 1987; 198(2):311-26. DOI: 10.1016/0022-2836(87)90315-9. View

17.

Warwicker J, Engelman B, Steitz T . Electrostatic calculations and model-building suggest that DNA bound to CAP is sharply bent. Proteins. 1987; 2(4):283-9. DOI: 10.1002/prot.340020404. View

18.

Berg O, von Hippel P . Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites. J Mol Biol. 1988; 200(4):709-23. DOI: 10.1016/0022-2836(88)90482-2. View

19.

Frederick C, QUIGLEY G, van der Marel G, VAN Boom J, Wang A, Rich A . Methylation of the EcoRI recognition site does not alter DNA conformation: the crystal structure of d(CGCGAm6ATTCGCG) at 2.0-A resolution. J Biol Chem. 1988; 263(33):17872-9. DOI: 10.2210/pdb4dnb/pdb. View

20.

Ebright R, Ebright Y, Gunasekera A . Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac DNA site. Nucleic Acids Res. 1989; 17(24):10295-305. PMC: 335301. DOI: 10.1093/nar/17.24.10295. View