Structurally Distinct Ubiquitin- and Sumo-Modified PCNA: Implications for Their Distinct Roles in the DNA Damage Response

• Published in: Structure (London) Vol. 23; no. 4; pp. 724 - 733
• Main Authors: Tsutakawa, Susan E., Yan, Chunli, Xu, Xiaojun, Weinacht, Christopher P., Freudenthal, Bret D., Yang, Kun, Zhuang, Zhihao, Washington, M. Todd, Tainer, John A., Ivanov, Ivaylo
• Format: Journal Article
• Language: English
• Published: United States Elsevier Ltd 07-04-2015; Elsevier
• Subjects: 60 APPLIED LIFE SCIENCES; Amino Acid Sequence; DNA Damage; DNA Repair; Molecular Dynamics Simulation; Molecular Sequence Data; Proliferating Cell Nuclear Antigen - chemistry; Proliferating Cell Nuclear Antigen - metabolism; Protein Binding; Saccharomyces cerevisiae - chemistry; Saccharomyces cerevisiae - enzymology; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - metabolism; SUMO-1 Protein - chemistry; SUMO-1 Protein - metabolism; Sumoylation
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2015.02.008

Proliferating cell nuclear antigen (PCNA) is a pivotal replication protein, which also controls cellular responses to DNA damage. Posttranslational modification of PCNA by SUMO and ubiquitin modulate these responses. How the modifiers alter PCNA-dependent DNA repair and damage tolerance pathways is largely unknown. We used hybrid methods to identify atomic models of PCNAK107-Ub and PCNAK164-SUMO consistent with small-angle X-ray scattering data of these complexes in solution. We show that SUMO and ubiquitin have distinct modes of association to PCNA. Ubiquitin adopts discrete docked binding positions. By contrast, SUMO associates by simple tethering and adopts extended flexible conformations. These structural differences are the result of the opposite electrostatic potentials of SUMO and Ub. The unexpected contrast in conformational behavior of Ub-PCNA and SUMO-PCNA has implications for interactions with partner proteins, interacting surfaces accessibility, and access points for pathway regulation.
[Display omitted]
•Ubiquitinated and SUMOylated PCNA complexes are structurally distinct in solution•Ubiquitin has segmental flexibility and occupies discrete positions on PCNA•SUMO associates by simple tethering and adopts extended flexible conformations•Distinct PTM-PCNA conformations underlie distinct roles in DNA damage response
Tsutakawa et al. combine computational modeling and small-angle X-ray scattering to show that SUMOylated and ubiquitinated PCNA have strikingly different conformations in solution due to opposite electrostatics of the modifiers. The distinct conformations underlie distinct roles for PCNA-Ub and PCNA-SUMO in DNA damage responses.