DNA clamp

Top and side views of a homotrimer of the human PCNA sliding clamp (rainbow colored, N-terminus = blue, C-terminus = red) with double stranded DNA modeled through the central pore (magenta).[1]
Cryo-EM structure of the DNA-bound PolD–PCNA processive complex
Structural basis for DNA binding by the PolD–PCNA complex

A DNA clamp, also known as a sliding clamp, is a protein complex that serves as a processivity-promoting factor in DNA replication. As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand. The clamp-polymerase protein–protein interactions are stronger and more specific than the direct interactions between the polymerase and the template DNA strand; because one of the rate-limiting steps in the DNA synthesis reaction is the association of the polymerase with the DNA template, the presence of the sliding clamp dramatically increases the number of nucleotides that the polymerase can add to the growing strand per association event. The presence of the DNA clamp can increase the rate of DNA synthesis up to 1,000-fold compared with a nonprocessive polymerase.[2]

  1. ^ PDB: 1W60​; Kontopidis G, Wu SY, Zheleva DI, Taylor P, McInnes C, Lane DP, et al. (February 2005). "Structural and biochemical studies of human proliferating cell nuclear antigen complexes provide a rationale for cyclin association and inhibitor design". Proceedings of the National Academy of Sciences of the United States of America. 102 (6): 1871–1876. doi:10.1073/pnas.0406540102. PMC 548533. PMID 15681588.
  2. ^ Mizrahi V, Henrie RN, Marlier JF, Johnson KA, Benkovic SJ (July 1985). "Rate-limiting steps in the DNA polymerase I reaction pathway". Biochemistry. 24 (15): 4010–4018. doi:10.1021/bi00336a031. PMID 3902078.