Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA Complex: Alteration of DNA binding specificity through alteration of DNA kinking

Journal of Molecular Biology

Volumn 314, Issue 1, 2001, Pages 75-82

  Chen, Shengfeng ^a   Vojtechovsky, Jaroslav ^a   Parkinson, Gary N ^a   Ebright, Richard H ^b   Berman, Helen M ^a  

^a RUTGERS UNIVERSITY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

CAMP receptor protein (CRP); Catabolite activator protein (CAP); Indirect readout; Protein DNA interaction; Protein induced DNA bending

Indexed keywords

CARBENE; CARBOXYLIC ACID; CURVED DNA; CYCLIC AMP BINDING PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; COMPLEX FORMATION; CRYSTALLOGRAPHY; DNA BINDING; DNA SEQUENCE; DNA STRUCTURE; HYDROGEN BOND; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; SEQUENCE ANALYSIS;

EID: 0035900557     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.2001.5090     Document Type: Article

References (25)

1. Crystal structure of a CAP-DNA complex: The DNA is bent by 90°
2. Structure of the CAP-DNA complex at 2.5 Å resolution: A complete picture of the protein-DNA interface
3. Aromatic hydrogen bond in sequence-specific protein-DNA recognition
4. Selection of DNA binding sites by regulatory proteins. The binding specificity of cyclic AMP receptor protein to recognition sites
5. Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus than for the E. coli lac DNA site
6. DNA sequence determinants for binding of the Escherichia coli catabolite gene activator protein
7. The change of DNA structure by specific binding of the cAMP receptor protein from rotation diffusion and dichroism measurements
8. The locus of sequence-directed and protein-induced DNA bending
9. The DNA binding domain and bending angle of E. coli CAP protein
10. The structure of B-DNA in oriented fibers
11. Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking
12. Mutations that alter the DNA sequence specificity of the catabolite gene activator protein of E. coli
13. Molecular basis of DNA sequence recognition by the catabolite gene activator protein: Detailed inferences from three mutations that alter DNA sequence specificity
14. 181]CAP
15. Identification of amino acid-base-pair contacts by genetic methods
16. The structure of a CAP-DNA complex having cAMP molecules bound to each monomer
17. 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
18. 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
19. Oscillation data reduction program
20. Data reduction
21. Crystallographic and NMR system: A new software suite for macromolecular structure determination
22. Improved methods for building protein models in electron density maps and the location of errors in these models
23. The Protein Data Bank
24. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
25. NUCPLOT: A program to generate schematic diagrams of protein-nucleic acid interactions