PDBsum entry 1em8

Gene regulation

PDB id: 1em8

Contents

Protein chains

147 a.a. *

110 a.a. *

Waters ×256

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Crystal structure of the chi:psi sub-Assembly of the escherichia coli DNA polymerase clamp-Loader complex.

Authors

J.M.Gulbis, S.L.Kazmirski, J.Finkelstein, Z.Kelman, M.O'Donnell, J.Kuriyan.

Ref.

Eur J Biochem, 2004, 271, 439-449. [DOI no: 10.1046/j.1432-1033.2003.03944.x]

PubMed id

14717711

Abstract

The chi (chi) and psi (psi) subunits of Escherichia coli DNA polymerase III form a heterodimer that is associated with the ATP-dependent clamp-loader machinery. In E. coli, the chi:psi heterodimer serves as a bridge between the clamp-loader complex and the single-stranded DNA-binding protein. We determined the crystal structure of the chi:psi heterodimer at 2.1 A resolution. Although neither chi (147 residues) nor psi (137 residues) bind to nucleotides, the fold of each protein is similar to the folds of mononucleotide-(chi) or dinucleotide-(psi) binding proteins, without marked similarity to the structures of the clamp-loader subunits. Genes encoding chi and psi proteins are found to be readily identifiable in several bacterial genomes and sequence alignments showed that residues at the chi:psi 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 chi:psi complex. One of the conserved regions was found to be located on chi, distal to the psi 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 psi (26 residues) that is disordered in the crystal structure. We speculate that psi is linked to the clamp-loader complex by this flexible, but conserved, N-terminal segment, and that the chi:psi unit is linked to the single-stranded DNA-binding protein via the distal surface of chi. The base of the clamp-loader complex has an open C-shaped structure, and the shape of the chi:psi complex is suggestive of a loose docking within the crevice formed by the open faces of the delta and delta' subunits of the clamp-loader.

Figure 4.
Fig. 4. Potential :single-stranded DNA-binding protein (SSB) interaction. A region of , with high sequence conservation, is shown (B). This surface is suggested to bind to the negatively charged C-terminal tail of SSB. Absolutely conserved and positively charged residues, located within this region, are shown on the left in a ribbon diagram in the same orientation (A). A schematic drawing of the inferred interaction between and the C-terminus consensus sequence of SSB is shown on the right (C).

Figure 5.
Fig. 5. Conservation of sequences in the N-terminal segment of . An alignment of the first 26 residues of , from the list of sequences given in Table 3, is shown. The alignment is colored according to the degree of sequence conservation. These 26 residues are disordered in the crystal structure of the : complex, yet a high amount of conservation is observed. It is proposed that the this linker binds to the clamp-loader complex, tethering the : heterodimer to the complex.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: Eur J Biochem (2004, 271, 439-449) copyright 2004.