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The p12 subunit of human polymerase δ uses an atypical PIP-box for molecular recognition of proliferating cell nuclear antigen (PCNA).

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posted on 15.08.2019, 15:04 by A Gonzalez-Magaña, A Ibáñez de Opakua, M Romano-Moreno, J Murciano-Calles, N Merino, I Luque, AL Rojas, S Onesti, FJ Blanco, A De Biasio
Human DNA polymerase δ is essential for DNA replication and acts in conjunction with the processivity factor proliferating cell nuclear antigen (PCNA). Besides its catalytic subunit (p125), pol δ comprises three regulatory subunits (p50, p68, and p12). PCNA interacts with all of these subunits, but only the interaction with p68 has been structurally characterized. Here, we report solution NMR-, isothermal titration calorimetry-, and X-ray crystallography-based analyses of the p12-PCNA interaction, which takes part in the modulation of the rate and fidelity of DNA synthesis by pol δ. We show that p12 binds with micromolar affinity to the classical PIP-binding pocket of PCNA via a highly atypical PIP-box located at the p12 N terminus. Unlike the canonical PIP-box of p68, the PIP-box of p12 lacks the conserved glutamine, binds through a 2-fork plug made of an isoleucine and a tyrosine residue at +3 and +8 positions, respectively, and is stabilized by an aspartate at +6 position, which creates a network of intra-molecular hydrogen bonds. These findings add to growing evidence that PCNA can bind a diverse range of protein sequences that may be broadly grouped as PIP-like motifs as has been previously suggested.

Funding

This work was supported by the Italian Association for Cancer Research (iCARE fellowship from AIRC and the European Commission to A. D. B. and AIRC Grant IG14718 to S. O.), by Grant CTQ2017-83810-R (MINECO/FEDER, UE; to F. J. B.), by MINECO Fellowship BES-2015-075847 (to A. G.-M.), and by Basque Government Predoctoral Fellowship PRE_2016_2_0249 (to M. R.-M.). The authors declare that they have no conflicts of interest with the contents of this article.

History

Citation

Journal of Biological Chemistry, 2019

Author affiliation

/Organisation/COLLEGE OF LIFE SCIENCES/Biological Sciences/Molecular & Cell Biology

Version

VoR (Version of Record)

Published in

Journal of Biological Chemistry

Publisher

American Society for Biochemistry and Molecular Biology

eissn

1083-351X

Acceptance date

17/01/2019

Copyright date

2019

Publisher version

http://www.jbc.org/content/294/11/3947

Notes

The atomic coordinates and structure factors (code 6HVO) have been deposited in the Protein Data Bank (http://wwpdb.org/). The NMR resonance data of this paper have been deposited in the Biological Magnetic Resonance Data Bank under BMRB accession codes 27661 and 27662, respectively.;The file associated with this record is under embargo until 12 months after publication, in accordance with the publisher's self-archiving policy. The full text may be available through the publisher links provided above.

Language

en