title: Structural similarity in the DNA-binding domains of catabolite gene activator and cro repressor proteins.
abstract: It is shown that there is a structural similarity between the presumed DNA-binding regions of the Escherichia coli catabolite gene activator protein ("CAP") and the cro repressor protein ("cro") from bacteriophage lambda. The correspondence between the two proteins is particularly striking for a structural unit consisting of two consecutive alpha-helices. The 24 alpha-carbon atoms that constitute the two-helical structural units in the two proteins can be superimposed with a root-mean-square disagreement of 1.1 A. It is shown that this agreement is very unlikely to be due to a chance correspondence. For both CAP activator and cro repressor proteins it is the second alpha-helix of the two-helical unit that has been proposed to bind within the major groove of left-handed or right-handed B DNA, respectively [McKay, D. B. & Steitz, T. A. (1981) Nature (London) 290, 744-749; Anderson, W. F., Ohlendorf, D. H., Takeda, Y. & Matthews, B. W. (1981) Nature (London) 290, 754-758]. The structural correspondence between CAP and cro seen here, together with other recent evidence of sequence homologies between cro, CAP, and other proteins that bind double-stranded DNA, suggests that the two-helical unit is likely to be a common feature of many DNA-binding proteins. The results also suggest that some principles of specific protein-double-stranded DNA interaction may be general and include recognition via alpha-helices fitting into the major groove of the DNA.
mesh_terms: D010582:Bacteriophage lambda; D001665:Binding Sites; D002352:Carrier Proteins; D004247:DNA; D004268:DNA-Binding Proteins; D004926:Escherichia coli; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011487:Protein Conformation; D011953:Receptors, Cyclic AMP; D012097:Repressor Proteins; D014157:Transcription Factors
chemical_list: D002352:Carrier Proteins; D004268:DNA-Binding Proteins; D011953:Receptors, Cyclic AMP; D012097:Repressor Proteins; D014157:Transcription Factors; D004247:DNA