The P1 phage replication protein RepA contacts an otherwise inaccessible thymine N3 proton by DNA distortion or base flipping

Nucleic Acids Research

Volumn 29, Issue 23, 2001, Pages 4892-4900

  Lyakhov, Ilya G ^a   Hengen, Paul N ^a,c   Rubens, Denise ^a   Schneider, Thomas D ^b  

^a SAIC FREDERICK INC   (United States)

^b NATIONAL CANCER INSTITUTE   (United States)

^c APPLIED BIOSYSTEMS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE NUCLEOTIDE; DNA; PROTON; PYRIMIDINE NUCLEOTIDE; REPLICATION PROTEIN A; THYMINE;

ARTICLE; BACTERIOPHAGE P1; BASE PAIRING; BINDING SITE; CELL ENERGY; CONTROLLED STUDY; DNA BINDING; DNA DAMAGE; DNA DENATURATION; DNA HELIX; DNA REPLICATION; GENETIC CONSERVATION; HYDROGEN BOND; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING;

EID: 0035581124     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/29.23.4892     Document Type: Article

References (33)

1. Sequence-specific recognition of double helical nucleic acids by proteins
2. Information analysis of sequences that bind the replication initiator RepA
3. Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation
4. P1 plasmid replication. Purification and DNA-binding activity of the replication protein RepA
5. Protein-DNA interactions in regulation of P1 plasmid replication
6. Missing-base and ethylation interference footprinting of P1 plasmid replication initiator
7. Reading of DNA sequence logos: Prediction of major groove binding by information theory
8. Crystal structure of an IHF-DNA complex: A protein-induced DNA U-turn
9. On base flipping
10. Base flipping
11. R promoter fusions
12. Monomerization of RepA dimers by heat shock proteins activates binding to DNA replication origin
13. Activation of DNA binding by the monomeric form of the P1 replication initiator RepA by heat shock proteins DnaJ and DnaK
14. A molecular chaperone, ClpA, functions like DnaK and DnaJ
15. Information content of binding sites on nucleotide sequences
16. Preparation and extraction of insoluble (inclusion-body) proteins from Escherichia coli
17. Most' compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: An extraordinarily stable structure resistant to nucleases and heat
18. Information analysis of Fis binding sites
19. The occurrence of C-H···O hydrogen bonds in proteins
20. C-H···O hydrogen bonding in biology
21. A role for C-H···O interactions in protein-DNA recognition
22. C-H···π-interactions in proteins
23. DNA bending: The prevalence of kinkiness and the virtues of normality
24. Conformation of the origin of P1 plasmid replication. Initiator protein induced wrapping and intrinsic unstacking
25. Searching for and predicting the activity of sites for DNA binding proteins: Compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF)
26. Three-dimensional structural views of damaged-DNA recognition: T4 endonuclease V, E. coli Vsr protein and human nucleotide excision repair factor XPA
27. DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity
28. The iteron bases and spacers of the P1 replication origin contain information that specifies the formation of a complex structure involved in initiation
29. A single DnaA box is sufficient for initiation from the P1 plasmid origin
30. Open-complex formation by the host initiator, DnaA at the origin of P1 plasmid replication
31. Replication control of plasmid P1 and its host chromosome: The common ground
32. Theory of molecular machines. II. Energy dissipation from molecular machines
33. Solvent-accessible surfaces of proteins and nucleic acids