Crystal structure of a DNA polymerase sliding clamp from a Gram-positive bacterium

Journal Article · Tue Jan 10 00:00:00 UTC 2006 · BMC Structural Biology (Online)

DOI: https://doi.org/10.1186/1472-6807-6-2 · OSTI ID:1626550

Argiriadi, Maria A. ^[1]; Goedken, Eric R. ^[2]; Bruck, Irina ^[3]; O'Donnell, Mike ^[3]; Kuriyan, John ^[2]

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1. Rockefeller Univ., New York, NY (United States). Howard Hughes Medical Inst.; DOE/OSTI
2. Univ. of California, Berkeley, CA (United States). Howard Hughes Medical Inst. Dept. of Chemistry; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences
3. Rockefeller Univ., New York, NY (United States). Howard Hughes Medical Inst.

Background: Sliding DNA clamps are processivity factors that are required for efficient DNA replication. DNA polymerases maintain proximity to nucleic acid templates by interacting with sliding clamps that encircle DNA and thereby link the polymerase enzyme to the DNA substrate. Although the structures of sliding clamps from Gram-negative bacteria (E. coli), eukaryotes, archaea, and T4-like bacteriophages are well-known, the structure of a sliding clamp from Grampositive bacteria has not been reported previously. Results: We have determined the crystal structure of the dimeric β subunit of the DNA polymerase III holoenzyme of Streptococcus pyogenes. The sliding clamp from this Gram-positive organism forms a ring-shaped dimeric assembly that is similar in overall structure to that of the sliding clamps from Gram-negative bacteria, bacteriophage T4, eukaryotes and archaea. The dimer has overall dimensions of ~90 Å × ~70 Å × ~25 Å with a central chamber that is large enough to accommodate duplex DNA. In comparison to the circular shape of other assemblies, the S. pyogenes clamp adopts a more elliptical structure. Conclusion: The sequences of sliding clamps from S. pyogenes and E. coli are only 23% identical, making the generation of structural models for the S. pyogenes clamp difficult in the absence of direct experimental information. Our structure of the S. pyogenes β subunit completes the catalog of clamp structures from all the major sequence grouping of sliding clamps. The more elliptical rather than circular structure of the S. pyogenes clamp implies that the topological nature of encircling DNA, rather than a precise geometric shape, is the most conserved aspect for this family of proteins.

• Research Organization: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
• Sponsoring Organization: National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
• Grant/Contract Number: AC02-05CH11231
• OSTI ID: 1626550
• Journal Information: BMC Structural Biology (Online), Journal Name: BMC Structural Biology (Online) Journal Issue: 1 Vol. 6; ISSN 1472-6807
• Publisher: BioMed CentralCopyright Statement
• Country of Publication: United States
• Language: English