Differential affinity and cooperativity functions of the amino-terminal 70 residues of λ integrase

Dibyendu Sarkar, Marco A. Azaro, Hideki Aihara, Christie V. Papagiannis, Radhakrishna Tirumalai, Simone E. Nunes-Düby, Reid C. Johnson, Tom Ellenberger, Arthur Landy

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29 Scopus citations


The site-specific recombinase (Int) of bacteriophage λ is a heterobivalent DNA-binding protein that binds two different classes of DNA-binding sites within its recombination target sites. The several functions of Int are apportioned between a large carboxy-terminal domain that cleaves and ligates DNA at each of its four "core-type" DNA-binding sites and a small amino-terminal domain, whose primary function is binding to each of its five "arm-type" DNA sites, which are distant from the core region. Int bridges between the two classes of binding sites are facilitated by accessory DNA-bending proteins that along with Int comprise higher-order recombinogenic complexes. We show here that although the 64 amino-terminal residues of Int bind efficiently to a single arm site, this protein cannot form doubly bound complexes on adjacent arm sites. However, 1-70 Int does show the same cooperative binding to adjacent arm sites as the full length protein. We also found that 1-70 Int specifies cooperative interactions with the accessory protein Xis when the two are bound to their adjacent cognate sites P2 and X1, respectively. To complement the finding that these two amino-terminal domain functions (along with arm DNA binding) are all specified by residues 1-70, we determined that Thr75 is the first residue of the minimal carboxy-terminal domain, thereby identifying a specific interdomain linker region. We have measured the affinity constants for Int binding to each of the five arm sites and the cooperativity factors for Int binding to the two pairs of adjacent arm sites, and we have identified several DNA structural features that contribute to the observed patterns of Int binding to arm sites. Taken together, the results highlight several interesting features of arm DNA binding that invite speculation about additional levels of complexity in the regulation of λ site-specific recombination.

Original languageEnglish (US)
Pages (from-to)775-789
Number of pages15
JournalJournal of Molecular Biology
Issue number4
StatePublished - 2002

Bibliographical note

Funding Information:
We thank Christine Lank and Gregg Gariepy for technical assistance, Joan Boyles for manuscript preparation, and members of the Landy laboratory for comments and suggestions. We are grateful to Jeffrey Gardner for communication of results prior to publication. We also thank Robert Weisberg, Gerald Koudelka, Don Crothers, Alex Rich and Dinshaw Patel for helpful discussions. This work was supported by NIH grants GM33928 and GM 62723 to A.L., NIH grant 59902 to T.E., and GM38509 to R.C.J.


  • DNA-binding protein
  • Protein-DNA interactions
  • Protein-protein interactions
  • Site-specific recombination


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