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X‐ray structure of T4 endonuclease VII: a DNA junction resolvase with a novel fold and unusual domain‐swapped dimer architecture
Author(s) -
Raaijmakers Hans,
Vix Olivier,
Törõ Imre,
Golz Stefan,
Kemper Börries,
Suck Dietrich
Publication year - 1999
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1093/emboj/18.6.1447
Subject(s) - holliday junction , dimer , biology , endonuclease , antiparallel (mathematics) , dna , recombinase , crystallography , stereochemistry , tn3 transposon , mutant , biochemistry , dna repair , chemistry , recombination , transposable element , physics , gene , organic chemistry , quantum mechanics , magnetic field
Phage T4 endonuclease VII (Endo VII), the first enzyme shown to resolve Holliday junctions, recognizes a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. We have determined the crystal structures of the Ca 2+ ‐bound wild‐type and the inactive N62D mutant enzymes at 2.4 and 2.1 Å, respectively. The Endo VII monomers form an elongated, highly intertwined molecular dimer exhibiting extreme domain swapping. The major dimerization elements are two pairs of antiparallel helices forming a novel ‘four‐helix cross’ motif. The unique monomer fold, almost completely lacking β‐sheet structure and containing a zinc ion tetrahedrally coordinated to four cysteines, does not resemble any of the known junction‐resolving enzymes, including the Escherichia coli RuvC and λ integrase‐type recombinases. The S‐shaped dimer has two ‘binding bays’ separated by ∼25 Å which are lined by positively charged residues and contain near their base residues known to be essential for activity. These include Asp40 and Asn62, which function as ligands for the bound calcium ions. A pronounced bipolar charge distribution suggests that branched DNA substrates bind to the positively charged face with the scissile phosphates located near the divalent cations. A model for the complex with a four‐way DNA junction is presented.