Crystal structure of the chi:psi subassembly of the Escherichia coli DNA polymerase clamp‐loader complex

• Published in: European journal of biochemistry Vol. 271; no. 2; pp. 439 - 449
• Main Authors: Gulbis, Jacqueline M., Kazmirski, Steven L., Finkelstein, Jeff, Kelman, Zvi, O'Donnell, Mike, Kuriyan, John
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Science Ltd 01.01.2004
• Subjects: clamp loader; DNA replication; Escherichia coli; processivity factor; sliding clamp
• ISSN: 0014-2956; 1432-1033
• DOI: 10.1046/j.1432-1033.2003.03944.x

The chi (χ) and psi (ψ) subunits of Escherichia coli DNA polymerase III form a heterodimer that is associated with the ATP‐dependent clamp‐loader machinery. In E. coli, the χ:ψ heterodimer serves as a bridge between the clamp‐loader complex and the single‐stranded DNA‐binding protein. We determined the crystal structure of the χ:ψ heterodimer at 2.1 Å resolution. Although neither χ (147 residues) nor ψ (137 residues) bind to nucleotides, the fold of each protein is similar to the folds of mononucleotide‐(χ) or dinucleotide‐(ψ) binding proteins, without marked similarity to the structures of the clamp‐loader subunits. Genes encoding χ and ψ proteins are found to be readily identifiable in several bacterial genomes and sequence alignments showed that residues at the χ:ψ interface are highly conserved in both proteins, suggesting that the heterodimeric interaction is of functional significance. The conservation of surface‐exposed residues is restricted to the interfacial region and to just two other regions in the χ:ψ complex. One of the conserved regions was found to be located on χ, distal to the ψ interaction region, and we identified this as the binding site for a C‐terminal segment of the single‐stranded DNA‐binding protein. The other region of sequence conservation is localized to an N‐terminal segment of ψ (26 residues) that is disordered in the crystal structure. We speculate that ψ is linked to the clamp‐loader complex by this flexible, but conserved, N‐terminal segment, and that the χ:ψ unit is linked to the single‐stranded DNA‐binding protein via the distal surface of χ. The base of the clamp‐loader complex has an open C‐shaped structure, and the shape of the χ:ψ complex is suggestive of a loose docking within the crevice formed by the open faces of the δ and δ′ subunits of the clamp‐loader.