STRUCTURE OF RESTRICTION-ENDONUCLEASE BAMHI PHASED AT 1.95-ANGSTROM RESOLUTION BY MAD ANALYSIS

Background: Type II restriction endonucleases recognize DNA sequences that vary between four to eight base pairs, and require only Mg2+ as a cofactor to catalyze the hydrolysis of DNA. Their protein sequences display a surprising lack of similarity, and no recurring structural motif analogous to the helix-tum-helix or the zinc finger of transcription factors, has yet been discovered. Results: We have determined the crystal structure of restriction endonuclease BamHI at 1.95 angstrom, resolution. The structure was solved by combining phase information derived from multi-wavelengh X-ray data by algebraic and maximum likelihood methods. The BamHI subunit consists of a central beta-sheet with alpha-helices on both sides. The dimer configuration reveals a large cleft which could accommodate B-form DNA. Mutants of the enzyme that are deficient in cleavage are located at or near the putative DNA-binding cleft. BamHI and endonuclease EcoRI share a common core motif (CCM) consisting of five beta-strands and two helices. It remains to be determined if other restriction enzymes also contain the CCM. Conclusions: The structure of BamHI provides the first clear evidence that there may be substantial structural homology amongst restriction enzymes, even though it is undetectable at the sequence level.