S. solfataricus DNA ligase is the fully open structure, in which the three domains are highly extended. In this work, the S. solfataricus ligase-PCNA complex was also analyzed by SAXS. S. solfataricus DNA ligase bound to the PCNA ring still retains an open, extended conformation. The closed, ring-shaped conformation observed in the Lig I structure as described above is probably the active form to catalyze a DNA end-joining reaction, and therefore, it is proposed that the open-to-closed movement occurs for ligation, and the switch in the conformational change is accommodated by a malleable interface with PCNA, which serves as an efficient platform for DNA ligation. the publication of these crystal structures, the three-dimensional structure of the ternary complex, consisting of DNA ligase-PCNA-DNA, using the P. furiosus proteins was obtained by EM single particle analysis. In the complex structure, the three domains of the crescent-shaped P. furiosus DNA ligase surround the central DNA duplex, encircled by the closed PCNA ring. The relative orientations of the ligase domains remarkably differ from those of the crystal structures, and therefore, a large domain rearrangement occurs upon ternary complex formation. the EM image model, the DNA ligase contacts PCNA at two sites, the conventional PIP box and a novel second contact in the middle adenylation domain. It is also interesting that a substantial DNA tilt from the PCNA ring axis is observed. Based on these structural analyses, a mechanism in which the PCNA binding proteins are bound and released sequentially. In fact, most of the PCNA binding proteins share the same binding sites in the interdomain connecting loop (IDCL) and the C-terminal tail of the PCNA. The structural features exclude the possibility that the three proteins contact the single PCNA ring simultaneously, because DNA ligase occupies two of the three subunits of the PCNA trimer. the case of the RFCPCNA-DNA complex structure obtained by the same EM technique, RFC entirely covers the PCNA ring, thus blocking the access of other proteins. These ternary complexes appear to favor a mechanism involving the sequential binding and release of replication factors.
12. Flap endonuclease 1 (FEN1)
processing of Okazaki fragments to make a continuous DNA strand is essential for the lagging strand synthesis in asymmetric DNA replication. The primase-synthesized RNA / DNA primers need to be removed to join the Okazaki fragments into an intact continuous strand DNA. Flap endonuclease 1 (FEN1) is mainly responsible for this task. Okazaki fragment maturation is highly coordinated with continuous DNA synthesis, and the interactions of DNA polymerase, FEN1, and DNA ligase with PCNA allow these enzymes to act sequentially during the maturation process, as described above. FEN1, a structure-specific 5-endonuclease, specifically recognizes a dsDNA with an unannealed 5-flap. the eukaryotic Okazaki fragment processing system, 5-flap DNA structures are formed by the strand displacement activity of DNA polymerase? . Lig I seals the nick after the flapped DNA is cleaved by FEN1. These processing steps are facilitated by PCNA. The interactions between eukaryotic FEN1 and PCNA have been well characterized, and the stimulatory effect of PCNA on the FE...
