(1) Abbott Laboratories, Research Computing and Information Sciences,
100 Abbott Park Road, Abbott Park, IL. 60064-3500
(2) Dept. of Microbiology, Duke University Medical Center,
Durham, NC 27710
In both prokaryotes and eucaryotes, the process of DNA replication can be separated into three phases: initiation, elongation, and termination. The first two phases of the process have been the subject of a great deal of study, while the final phase has just begun to garner attention. In several organisms termination of DNA replication does not seem to involve any coordinated mechanism and occurs at random positions along the organism's chromosome. In both Escherichia coli and Bacillus subtilis, the process is not random and instead occurs at precisely defined regions interspersed along the circular chromosome. Studies have shown that the controlled termination in these prokaryotes is fully dependent on a class of sequence-specific DNA-binding proteins known as "terminator" proteins. In E. coli, the terminator protein is known as ter or tus, while in B. subtilis, the terminator protein has been dubbed the replication terminator protein or RTP. Current models for termination of DNA replication are based on data gathered mainly from molecular biological and biochemical studies. To extend these models, the atomic-resolution structure of one of these proteins was investigated by X-ray crystallography. The protein in question, the replication terminator protein (RTP), was solved by MIR (1) and refined to a resolution of 2 Angstroms. This provided the first view of the structure of a terminator protein.
The replication terminator protein exists as a symmetric dimer and is in the alpha+beta protein- folding class. The protein has several uncommon features, such as an anti-parallel coiled-coil dimerization domain, and it is possible to rationalize several features of the termination systems with the structure of the protein. It was possible to construct a molecular model of the protein-DNA interactions, and genetic and biochemical studies were initiated to confirm this model. The structures of several biologically significant point-mutants of RTP were also investigated by X-ray crystallography. Finally, both biochemical cleavage data and computational docking were incorporated to reconstruct the interaction of RTP with the entire cognate DNA sequence; this data was also used to construct a cogent structure-based model for the termination of DNA replication by RTP.
1. Bussiere, D.E., et al. Crystal structure of the Replication Terminator Protein from Bacillus subtilis at 2.6 Angstroms. Cell 80: 651-660.