Crystal structure of an archaeal DNA sliding clamp: proliferating cell nuclear antigen from Pyrococcus furiosus - PubMed (original) (raw)

Crystal structure of an archaeal DNA sliding clamp: proliferating cell nuclear antigen from Pyrococcus furiosus

S Matsumiya et al. Protein Sci. 2001 Jan.

Abstract

The proliferating cell nuclear antigen (PCNA) is now recognized as one of the key proteins in DNA metabolic events because of its direct interactions with many proteins involved in important cellular processes. We have determined the crystal structure of PCNA from a hyperthermophilic archaeon, Pyrococcus furiosus (pfuPCNA), at 2.1 A resolution. pfuPCNA forms a toroidal, ring-shaped structure consisting of homotrimeric molecules, which is also observed in the PCNA crystals from human and yeast. The overall structure of pfuPCNA is highly conserved with other PCNA proteins, as well as with the bacterial ss clamp and the bacteriophage gp45. This result shows that the three-dimensional structure of the sliding clamp is conserved in the three domains of life. pfuPCNA has two remarkable features compared with the human and yeast PCNA molecules: it has more ion pairs and fewer intermolecular main chain hydrogen bonds. The former may contribute to the thermal stability of pfuPCNA, and the latter may be the cause of the stimulatory effect of pfuPCNA on the DNA synthesizing activity of P. furiosus DNA polymerases in the absence of the clamp loader replication factor C in vitro.

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Figures

Fig. 1.

Fig. 1.

Amino acid sequence alignment of _Pfu_PCNA with yeast and human PCNA. The secondary structure elements determined from the crystal structure are labeled and indicated (black for α helices and gray for β strands).

Fig. 2.

Fig. 2.

A ribbon diagram of _Pfu_PCNA. The N-terminal domain is shown in light gray, and the C-terminal domain is shown in dark gray.

Fig. 3.

Fig. 3.

Comparison of sliding clamps from the three domains of life. (Left) _Pfu_PCNA trimer, (center) yeast PCNA trimer (Krishna et al. 1994, PDB code 1PLQ), and (right) E. coli β subunit dimer (Kong et al. 1992, PDB code 2POL).

Fig. 4.

Fig. 4.

Comparison of main-chain hydrogen bonds at the intermolecular interface. (Left) _Pfu_PCNA, (center) yeast PCNA, and (right) human PCNA (Gulbis et al. 1996, PDB code 1AXC).

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