Biochemical analysis of the yeast condensin Smc2/4 complex: an ATPase that promotes knotting of circular DNA

J Biol Chem. 2003 Jul 11;278(28):26238-48. doi: 10.1074/jbc.M302699200. Epub 2003 Apr 28.

Abstract

To better understand the contributions that the structural maintenance of chromosome proteins (SMCs) make to condensin activity, we have tested a number of biochemical, biophysical, and DNA-associated attributes of the Smc2p-Smc4p pair from budding yeast. Smc2p and Smc4p form a stable heterodimer, the "Smc2/4 complex," which upon analysis by sedimentation equilibrium appears to reversibly self-associate to form heterotetramers. Individually, neither Smc2p nor Smc4p hydrolyzes ATP; however, ATPase activity is recovered by equal molar mixing of both purified proteins. Hydrolysis activity is unaffected by the presence of DNA. Smc2/4 binds both linearized and circular plasmids, and the binding appears to be independent of adenylate nucleotide. High mole ratios of Smc2/4 to plasmid promote a geometric change in circular DNA that can be trapped as knots by type II topoisomerases but not as supercoils by a type I topoisomerase. Binding titration analyses reveal that two Smc2/4-DNA-bound states exist, one disrupted by and one resistant to salt challenge. Competition-displacement experiments show that Smc2/4-DNA-bound species formed at even high protein to DNA mole ratios remain reversible. Surprisingly, only linear and supercoiled DNA, not nicked-circular DNA, can completely displace Smc2/4 prebound to a labeled, nicked-circular DNA. To explain this geometry-dependent competition, we present two models of DNA binding by SMCs in which two DNA duplexes are captured within the inter-coil space of an Smc2/4 heterodimer. Based on these models, we propose a DNA displacement mechanism to explain how differences in geometry could affect the competitive potential of DNA.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenosine Triphosphatases / metabolism
  • Adenosine Triphosphate / metabolism
  • Adenosine Triphosphate / pharmacology
  • Animals
  • Binding, Competitive
  • Carrier Proteins / metabolism*
  • Cell Cycle Proteins
  • Chromosomal Proteins, Non-Histone / metabolism*
  • DNA / chemistry*
  • DNA / metabolism
  • DNA, Circular
  • Dimerization
  • Dose-Response Relationship, Drug
  • Electrophoresis, Polyacrylamide Gel
  • Genetic Complementation Test
  • Hydrolysis
  • Kinetics
  • Models, Molecular
  • Nuclear Proteins / metabolism*
  • Plasmids / metabolism
  • Protein Binding
  • Protein Conformation
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Ultraviolet Rays
  • Xenopus / metabolism

Substances

  • Carrier Proteins
  • Cell Cycle Proteins
  • Chromosomal Proteins, Non-Histone
  • DNA, Circular
  • Nuclear Proteins
  • SMC2 protein, S cerevisiae
  • SMC4 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • Adenosine Triphosphate
  • DNA
  • Adenosine Triphosphatases