Structural study on the Smc subunit of prokaryotic condensin

Abstract

Structural Maintenance of Chromosome (SMC) complexes are involved in various cellular mechanisms that require chromosomal stability, such as regulation of chromosomal superstructure formation and chromosome segregation during cell division. Condensin, one of the SMC family protein complexes, is present in prokaryotes as well as in eukaryotes, and performs essential functions for DNA condensation and segregation. The SMC subunit of condensin consists of “head” domain that functions as an ABC ATPase and a “hinge” domain that mediates homo- or hetero-dimerization of SMC. These two domains are connected through a 49 nm coiled-coil “arm”. SMC is believed to translocate on chromosomes through a unique cyclic process of its head domains that is coupled to ATP hydrolysis. A pair of heads forms a transient dimer through sandwiching two molecules of ATP, and returns to separated monomers after the hydrolysis reaction. However, it was unknown how the ATP hydrolysis is related to the mechanical motions of SMC on DNA. In addition, the structural information of the coiled-coil arm is limited to the parts adjacent to the SMC head and hinge domain. This study elucidates the whole structure of prokaryotic Smc protein dimer using protein crystallography and high-throughput cysteine cross-linking study. Five crystal structures were determined: three fragments of Pyrococcus Smc, and two fragments of Bacillus subtilis Smc. Together with the cross-linking data, the structural reconstitution revealed that Smc adopts a rod-shaped homodimer with the two closely juxtaposed coiled-coil arms, which close the inter-arm space. This rigid rod conformation of SMC arms results in a misaligned position of the ATP-binding pockets of the two head domains. In order to bind ATP, head domains require rotational and translational movements, which induce consequent opening of Smc arms. These observations suggest a new mechanistic model for the DNA condensation where condensin targets the loading site and pulls out DNA loops through its successive mechanochemical gating.