Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn.
Integration host factor (IHF) is a small heterodimeric protein that specifically binds to DNA and functions as an architectural factor in many cellular processes in prokaryotes. Here, we report the crystal structure of IHF complexed with 35 bp of DNA. The DNA is wrapped around the protein and bent by >160 degrees, thus reversing the direction of the helix axis within a very short distance. Much of the bending occurs at two large kinks where the base stacking is interrupted by intercalation of a proline residue. IHF contacts the DNA exclusively via the phosphodiester backbone and the minor groove and relies heavily on indirect readout to recognize its binding sequence. One such readout involves a six-base A tract, providing evidence for the importance of a narrow minor groove.
Rice
P A
PA
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
Yang
S
S
Mizuuchi
K
K
Nash
H A
HA
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000648:ultrastructure*; D010582:Bacteriophage lambda; D018360:Crystallography, X-Ray; D004279:DNA, Viral; D004268:DNA-Binding Proteins / Q000648:ultrastructure*; D003852:Deoxyribonucleoproteins / Q000648:ultrastructure; D004926:Escherichia coli / Q000737:chemistry; D034982:Integration Host Factors; D007364:Intercalating Agents; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011392:Proline / Q000737:chemistry
D001426:Bacterial Proteins; D004279:DNA, Viral; D004268:DNA-Binding Proteins; D003852:Deoxyribonucleoproteins; D034982:Integration Host Factors; D007364:Intercalating Agents; D011392:Proline