Nucleic Acids Research, 1994, Vol. 22, No. 16 3397-3405
© 1994
STRUCTURAL BIOLOGY |
Stereochemical basis of DNA recognition by Zn fingers
MRC Laboratory of Molecular Biology Hills Road, Cambridge, CB2 2QH, UK, 1Beckman Laboratories for Structural Biology, Department of Cell Biology, Stanford Medical School CA 94305-5400, USA 2Schole of medicine, Tohoku University Seiryo-machi, Sendai, 980–77, Japan
* To whom correspondence should be addressed
Received April 25, 1994. Revised July 5, 1994. Accepted July 5, 1994.
DNA-recognition rules for Zn fingers are discussed in terms of crystal structures. The rules can explain the DNA-binding characteristics of a number of Zn finger proteins for which there are no crystal structures. The rules have two parts: chemical rules, which list the possible pairings between the 4 DNA bases and the 20 amino acid residues, and stereochemical rules, which describe the specific base positions contacted by several amino acid positions in the Zn finger. It is discussed that to maintain the correct binding geometry, in which the N-terminus of the recognition helix is closer to the DNA than the C-terminus, the residues facing the DNA on the helix must be larger near the C-terminus, and that two different types of fingers (A and B) bind to DNA in distinctly different ways and cover different numbers of base pairs.
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