Physical basis of a protein-DNA recognition code

Current Opinion in Structural Biology

Volumn 7, Issue 1, 1997, Pages 117-125

  Choo, Yen ^a   Klug, Aaron ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA BINDING PROTEIN;

BINDING SITE; CRYSTAL STRUCTURE; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; REVIEW; STEREOCHEMISTRY;

EID: 0031042082     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80015-2     Document Type: Article

References (39)

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39. Houbaviy HB, Usheva A, Shenk T, Burley SK. Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator. of special interest Proc Natl Acad Sci USA. 93:1996;13577-13582 The cocrystal structure of the four zinc fingers from YY1 protein bound to the adeno-associated virus P5 initiator DNA reveals Zif268-like binding by fingers 3 and 4, whereas finger 1 is seen to make a full complement of phosphate contacts but only one contact to a DNA base. Finger 2 shows a remarkable mode of binding where a canonical arginine - guanine contact at position 6 occurs alongside an unusual lysine - guanine contact from position 3. The use of a long amino acid at position 3 forces the zinc finger to stand parallel to the DNA axis, distancing position -1 from the 'bound' strand such that it contacts the complementary strand two base steps along the helix. The mechanism of strand switching by this zinc finger illustrates yet another binding mode available to this versatile motif, and this particular case it is proposed to play an important role in establishing the polarity of transcription from the initiator element.