Restriction endonuclease BamHI/DNA complex
Bacillus amyloliquefaciens (bacteria)
Type II restriction endonucleases, along with their associated methyltransferases, are essential components of the restriction-modification systems commonly found in bacteria. Their function is to protect the bacteria against invading DNA but, due to their exquisite specificity, they have also become powerful tools of modern biotechnology. Almost 2,400 type II restriction enzymes representing 188 different specificities have so far been discovered. They generally recognize DNA sequences that vary from four to eight base pairs (bp) in length and cleave DNA within or close to the recognition sequences, and require only magnesium ion to catalyze the hydrolysis of DNA.
Bam HI endonuclease binds as a dimer to the symmetrical sequence 5'-GGATCC-3'. The enzyme cleaves DNA after the 5'-G on each strand to produce 4-bp (5') staggered ends. The structure of Bam HI bound to a 12-bp DNA fragment containing its recognition sequence was determined at 2.2 angstrom resolution. The DNA binds in the large cleft of the Bam HI dimer while retaining a regular B-DNA-like conformation without major bends or kinks. Upon DNA binding the enzyme undergoes a series of conformational changes. The most striking conformational change is the unraveling of carboxyl-terminal alpha helices to form partially disordered 'arms'. The arm from one subunit fits into the minor groove while the arm from the symmetry related subunit follows the DNA sugar-phosphate backbone. Although Bam HI shares structural similarity with endonuclease Eco RI cleaving the sequence 5'-GAATTC-3', none of the interactions could have been anticipated from the Eco RI-DNA complex. Recognition of DNA base pairs occurs primarily in the major groove, with a few interactions occurring in the minor groove. The complex also provides new insight into the mechanism by which the enzyme catalyzes the hydrolysis of DNA phosphodiester groups.
Protein Data Bank (PDB)
author: Naoyuki Miyazaki