Structural studies of protein–nucleic acid interaction: the sources of sequence-specific binding

Abstract

Structural studies of DNA-binding proteins and their complexes with DNA have proceeded at an accelerating pace in recent years due to important technical advances in molecular genetics, DNA synthesis, protein crystallography and nuclear magnetic resonance. The last major review on this subject by Pabo & Sauer (1984) summarized the structural and functional studies of the three sequence-specific DNA-binding proteins whose crystal structures were then known, the E. coli catabolite gene activator protein (CAP) (McKay & Steitz, 1981; McKay et al.1982; Weber & Steitz, 1987), a cro repressor from phage λ (Anderson et al.1981), and the DNA-binding proteolytic fragment of λcI repressor protein (Pabo & Lewis, 1982) Although crystallographic studies of the E. coli lac repressor protein were initiated as early as 1971 when it was the only regulatory protein available in sufficient quantities for structural studies (Steitz et al.1974), little was established about the structural aspects of DNA-binding proteins until the structure of CAP was determined in 1980 followed shortly thereafter by the structure of λcro repressor and subsequently that of the λ repressor fragment. There are now determined at high resolution the crystal structures of seven prokaryotic gene regulatory proteins or fragments [CAP,λcro,λcI repressor fragment, 434 repressor fragment (Anderson et al.1987), 434 cro repressor (Wolberger et al.1988),E. coli trp repressor (Schevitz et al.1985),E. coli met repressor (Rafferty et al.1989)],EcoR I restriction endonuclease (McClarin et al.1986), DNAse I (Suck & Ofner, 1986), the catalytic domain of γδ resolvase (Hatfull et al.1989) and two sequence-independent double-stranded DNA-binding proteins [the Klenow fragment of E. coli DNA polymerase I (Ollis et al.1985) and the E. coli Hu protein (Tanaka et al., 1984)].