1EM8

Crystal structure of chi and psi subunit heterodimer from DNA POL III

PDB DOI: 10.2210/pdb1EM8/pdb

Classification: GENE REGULATION
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2000-03-16 Released: 2003-08-26
Deposition Author(s): Gulbis, J.M., Finkelstein, J., O'Donnell, M., Kuriyan, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.265
R-Value Work: 0.229
R-Value Observed: 0.233

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the chi:psi sub-assembly of the Escherichia coli DNA polymerase clamp-loader complex.

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

(2004) Eur J Biochem 271: 439-449

PubMed: 14717711 Search on PubMed
DOI: 10.1046/j.1432-1033.2003.03944.x
Primary Citation of Related Structures:
1EM8

PubMed 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.

Organizational Affiliation:

Laboratory of Molecular Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE III CHI SUBUNIT	A, C	147	Escherichia coli	Mutation(s): 0 EC: 2.7.7.7
UniProt
Find proteins for P28905 (Escherichia coli (strain K12)) Explore P28905 Go to UniProtKB: P28905
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28905
Protein Feature View Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE III PSI SUBUNIT	B, D	112	Escherichia coli	Mutation(s): 0 EC: 2.7.7.7
UniProt
Find proteins for P28632 (Escherichia coli (strain K12)) Explore P28632 Go to UniProtKB: P28632
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28632
Protein Feature View Expand
Reference Sequence