Location of enzymatic and DNA-binding domains on E. coli protease La

Escherichia coli protease La is an ATP-dependent enzyme that has a DNA-binding site. The locations of the enzymatic and DNA-binding sites are not known. We report that a 75-residue segment at the carboxy-terminus of the protease La is similar to part of Bacillus licheniformis beta-lactamase, a serine enzyme. The comparison score is 8.2 standard deviations higher than that obtained with 10,000 comparisons of randomized sequences of these segments. The probability of obtaining such a score by chance is 1.2 x 10(-16). We also find that a 107-residue segment in the amino-terminus half of protease La is similar to part of the sopB protein, a DNA-binding protein of the plasmid F of E. coli. The comparison score for these segments is 8 standard deviations (P = 6 x 10(-16)). These strong amino acid sequence similarities suggest the locations of the catalytic serine and the DNA-binding domains of protease La.