Alternating zinc fingers in the human male associated protein ZFY: 2D NMR structure of an even finger and implications for "jumping-linker" DNA recognition.
ZFY, a sex-related Zn-finger protein encoded by the human Y chromosome, is distinguished from the general class of Zn-finger proteins by the presence of a two-finger repeat. Whereas odd-numbered domains and linkers fit a general consensus, even-numbered domains and linkers exhibit systematic differences. Because this alternation may have fundamental implications for the mechanism of protein-DNA recognition, we have undertaken biochemical and structural studies of fragments of ZFY. We describe here the solution structure of a representative nonconsensus (even-numbered) Zn finger based on 2D NMR studies of a 30-residue peptide. Structural modeling by distance geometry and simulated annealing (DG/SA) demonstrates that this peptide folds as a miniglobular domain containing a C-terminal beta--hairpin and N-terminal alpha-helix (beta beta alpha motif). These features are similar to (but not identical with) those previously described in consensus-type Zn fingers (derived from ADR1 and Xfin); the similarities suggest that even and odd ZFY domains bind DNA by a common mechanism. A model of the protein-DNA complex (designated the "jumping-linker" model) is presented and discussed in terms of the ZFY two-finger repeat. In this model every other linker is proposed to cross the minor groove by means of a putative finger/linker submotif HX4HX3-hydrophobic residue-X3. Analogous use of a hydrophobic residue in a linker that spans the minor groove has recently been described in crystallographic and 3D NMR studies of homeodomain-DNA complexes. The proposed model of ZFY is supported in part by the hydroxyl radical footprint of the TFIIIA-DNA complex [Churchill, M.E.A., Tullius, T.D., & Klug, A. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 5528-5532].
Kochoyan
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Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115.
Havel
T F
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Nguyen
D T
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Dahl
C E
CE
Keutmann
H T
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Weiss
M A
MA
D000595:Amino Acid Sequence; D003196:Computer Graphics; D004268:DNA-Binding Proteins / Q000737:chemistry*; D006801:Humans; D006878:Hydroxides; D017665:Hydroxyl Radical; D051741:Kruppel-Like Transcription Factors; D009682:Magnetic Resonance Spectroscopy; D008297:Male; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D012995:Solubility; D013113:Spin Labels; D035582:Transcription Factor TFIIIA; D014157:Transcription Factors / Q000235:genetics; D015032:Zinc / Q000737:chemistry; D016335:Zinc Fingers / Q000235:genetics*
D004268:DNA-Binding Proteins; D006878:Hydroxides; D051741:Kruppel-Like Transcription Factors; D013113:Spin Labels; D035582:Transcription Factor TFIIIA; D014157:Transcription Factors; C054430:ZFY protein, human; D017665:Hydroxyl Radical; D015032:Zinc