Protein-Dna Recognition

Abstract

Several general principles emerge from the studies of Cro, lambda repressor, and CAP. The DNA-binding sites are recognized in a form similar to B-DNA. They do not form cruciforms or other novel DNA structures. There seem to be proteins that bind left-handed Z-DNA (87) and DNA in other conformations, but it remains to be seen how these structures are recognized or how proteins recognize specific sequences in single-stranded DNA. Cro, repressor, and CAP use symmetrically related subunits to interact with two-fold related sites in the operator sequences. Many other DNA-binding proteins are dimers or tetramers and their operator sequences have approximate two-fold symmetry. It seems likely that these proteins will, like Cro, repressor, and CAP, form symmetric complexes. However, there is no requirement for symmetry in protein-DNA interactions. Some sequence-specific DNA-binding proteins, like RNA polymerase, do not have symmetrically related subunits and do not bind to symmetric recognition sequences. Cro, repressor, and CAP use alpha-helices for many of the contacts between side chains and bases in the major groove. An adjacent alpha-helical region contacts the DNA backbone and may help to orient the "recognition" helices. This use of alpha-helical regions for DNA binding appears to be a common mode of recognition. Most of the contacts made by Cro, repressor, and CAP occur on one side of the double helix. However, lambda repressor contacts both sides of the double helix by using a flexible region of protein to wrap around the DNA. Recognition of specific base sequences involves hydrogen bonds and van der Waals interactions between side chains and the edges of base pairs. These specific interactions, together with backbone interactions and electrostatic interactions, stabilize the protein-DNA complexes. The current models for the complexes of Cro, repressor, and CAP with operator DNA are probably fundamentally correct, but it should be emphasized that model building alone, even when coupled with genetic and biochemical studies, cannot be expected to provide a completely reliable "high-resolution" view of the protein-DNA complex. For example, the use of standard B-DNA geometry for the operator is clearly an approximation.(ABSTRACT TRUNCATED AT 400 WORDS)

Complete nucleotide sequence of theEscherichia coli recBgene

“…Further work will be required to elucidate the mechanisms of transciption of these genes. The deduced RecEB amino acid sequence contains a consensus ATP binding site (39), and a predicted helix-turn-helix structure implicated in DNA binding (42), in agreement with the experimental observations that the RecB protein has DNA-dependent ATPase activity (19) and binds tightly to single stranded DNA.…”

Structural aspects of protein-DNA recognition

“…The structure shows that the protein binds to the operator site symmetrically, in accordance with the two-fold symmetry of the operator site, with one helix (helix 3) from each subunit fitting into the major groove of each half-site and the N-terminal arm of each monomer wrapping around the DNA making contacts with the central base-pairs of the operator site, as had previously been proposed ( Fig. 9; Pabo & Sauer, 1984). The structure of the monomer in the co-crystal complex shows no significant differences to that of the monomer in the absence of DNA and the conformation of the DNA fits with the general geometric constraints of B-DNA with no noticeable distortions (Jordan & Pabo, 1988).…”

“…1) lies in the major groove, providing sequence-specific DNA interactions and is termed the recognition helix. The N-termini of both helices point towards the phosphate backbone, using the positive helix-dipole for the correct positioning of the recognition helix (Pabo & Sauer, 1984;Brennan & Matthews, 1989a). It is presumed that the amino acid side chains jutting out of the recognition helix are able to make sequence-specific interactions with exposed functional groups in the major groove of the DNA.…”

“…The proteins listed in (Ptashne, 1986 chemical and genetic studies (reviewed in Pabo & Sauer, 1984;Ptashne, 1986), have shown that the N-terminal domain (92 amino acids) of ACI repressor binds to its operator sites as a dimer and that DNA recognition and transcriptional regulation can be altered by mutations of amino acids within this domain. A cro repressor also binds to the same operator sites as a dimer, although both proteins show little amino acid sequence similarity.…”

Families of bacterial signal‐transducing proteins

“…2). The regulator domain frequently contains a helix-turn-helix motif typical of DNA-binding proteins (Pabo and Sauer, 1984).…”