Structure of the Recombination Protein RuvA and a model for its Binding to Holliday Junction

J.B.Rafferty, S.E.Sedelnikova, D.Hargreaves, P.J.Artymiuk, P.J.Baker, G.J.Sharples, A.A.Mahdi, R.G.Lloyd and D.W.Rice
Science 274, (1996)
Krebs Institute, University of Sheffield
Department of Genetics, University of Nottingham

DNA animation, (c)KI Animated model of the motion of the DNA bases at a four-way DNA-duplex crossover, or Holliday junction, when bound to the protein RuvA during branch migration. The junctions are formed by homologous recombination as part of DNA repair and replication processes. Branch migration and junction resolution are catalyzed by the action of the RuvA, RuvB and RuvC proteins in E.coli. The DNA has been modelled in a square-planar configuration and fitted onto the recently determined structure of the RuvA protein which binds its DNA substrate in a structure-specific manner and acts as a scaffold to organize the arrangement of the duplex arms. The DNA alone is shown in here, for clarity, to emphasize the rotation of the duplexes and translocation of the bases between the arms of the junction.

RuvA/Holliday Junction complex Model

RuvA/DNA complex animation, (c)KI A model has been constructed for the interaction of RuvA with its DNA target using a simple model of a Holliday junction in which the double-stranded B-DNA arms are held in a square-planar arrangement. The protein and junction have been docked manually maintaining colinearity of their respective fourfold axes. A good fit of the DNA onto the protein as judged by complementarity of their surface shapes and charges was observed when the axes of the DNA helical arms lay along the grooves in the concave surface of the protein. The pairs of parent and daughter duplexes are on opposite sides of the central pin which is positioned such that the strands of the incoming duplex DNA are encouraged to separate. The strands are then channelled into orthogonal grooves in the protein surface where they anneal with base pairs from the other incoming parent DNA duplex to form the outgoing daughter duplexes.

RuvA, RuvB & DNA complex

RuvA, RuvB, DNA complex, (c)KI A simple model of a RuvA/RuvB/DNA complex extrapolating from the above model and in agreement with the electron microscopy results of Parsons et al. (Nature 374, 375 (1995)). RuvA binds the Holliday junction at the central crossover point and targets two RuvB hexamers onto opposite arms of the DNA where they encircle the DNA duplexes and facilitate branch migration in concert with RuvA in an ATP dependent manner.

  • enlarged image
  • Details of the structure of RuvA and its DNA binding surface