Nucleotide-Induced Conformational Changes in an Isolated Escherichia coli DNA Polymerase III Clamp Loader Subunit

Marjetka Podobnik, Tanya F. Weitze, Mike O’Donnell and John Kuriyan

Structure (2003) March(11): 253-–26 (local copy)

Abstract / Figures from the paper / PDB coordinates /


Sliding clamps are loaded onto DNA by ATP-driven clamp loader complexes. The structure of the E. coli clamp loader in a nucleotide-free state has been determined previously (Jeruzalmi et al. (2001), Cell 106, 429-441). We now report crystal structures of a truncated form of the isolated ?-ATPase subunit, ?1-243, of the E. coli clamp loader, in nucleotide-free and bound forms. Our analysis of ?1-243 has revealed a systematic conformational difference between the empty and nucleotide bound forms of the ? subunit. This involves a change in the relative orientation between Domains I and II, which results in an opening of the nucleotide binding site and a change in the shape of the ? subunit that appears sufficient to rupture the tight interaction between two of the ? subunits in the empty complex. Our studies with the isolated ? subunit show that both ATP and ADP are able to induce similar transitions from a closed to an open form of the ATPase subunit. The ability of ATP, but not ADP, to drive clamp loading must therefore arise from interfacial interactions in the assembled clamp loader that distinguish between the subunits. Further experiments including all the subunits of the clamp loader complex (in the absence or presence of the sliding clamp) are needed to fully characterize the sequence of events upon the binding of the nucleotides at the subunit interfaces, to understand the role of conformational changes and the residues at those interfaces in the process of loading the sliding clamps onto DNA.

Illustrations from the paper. Click on the small image to get a bigger one.

PDB Coordinates

1NJF. Nucleotide Bound Form Of An Isolated E. Coli Clamp Loader gamma Subunit (local copy)

1NJG. Nucleotide-Free Form Of An Isolated E. Coli Clamp Loader gamma Subunit (local copy)