Interaction of Terminase, the DNA Packaging Enzyme of Phage λ, with itscosDNA Substrate

Terminase, the DNA packaging enzyme of phage λ is an ATP-stimulated, site-specific endonuclease comprising the products of λ genesNu1 andA. The interaction of terminase with its specific DNA substratecoswas studied by footprinting.cos(the DNA segmentR4-cosN-R3R2R1), situated at the chromosomal junctions in a concatemer, consists of a nicking domain (cosN) where terminase nicks DNA to regenerate the 12-base cohesive ends of the mature λ chromosome and a binding domain (cosB) that includes four 16-base-pair repeat sequences,R1, R2andR3to the right ofcosNandR4 (now calledcosQand not, in strict definition, part ofcosB) to the left ofcosN. We show that terminase molecules bind asymmetrically to the two ends of the chromosome. Binding to the right ofcosNis stimulated by ATP, whereas binding to the left ofcosNis strictly dependent upon ATP. WhencosNis deleted and ATP is withheld, terminase molecules bind exclusively to theR3,R2andR1sitesviatheir gpNu1 subunits. An invariantR-site GG doublet is protected from methylation in bothR3andR, showing the location of major-groove close contacts upon binding. Terminase's interactions with DNAs that include all ofcosare more extensive and are influenced by ATP; not only are theRsites protected, but so is the DNA between them, as well ascosN,thecosN-R3region,R4and sequences to the left ofR4. The pattern suggests an highly organized protein-DNA continuum involving several terminase molecules and several hundred base-pairs of DNA, suitably named the termisome. Evidence is given that this assembly is dependent on the interaction of ATP with the gpA subunit of terminase.