A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp

Amanda S Altieri; Jane E Ladner; Zhuo Li; Howard Robinson; Zahur F Sallman; John P Marino; Zvi Kelman

doi:10.1093/nar/gkw351

A small protein inhibits proliferating cell nuclear antigen by breaking the DNA clamp

Nucleic Acids Res. 2016 Jul 27;44(13):6232-41. doi: 10.1093/nar/gkw351. Epub 2016 May 3.

Authors

Amanda S Altieri¹, Jane E Ladner¹, Zhuo Li², Howard Robinson³, Zahur F Sallman⁴, John P Marino¹, Zvi Kelman⁵

Affiliations

¹ Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
² Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA Third Institute of Oceanography, State Oceanic Administration, 184 Daxue Road, Xiamen, Fujian 361005, China.
³ National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY 11973, USA.
⁴ Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
⁵ Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA Biomolecular Labeling Laboratory, Institute for Bioscience and Biotechnology Research, University of Maryland and the National Institute of Standards and Technology, 9600 Gudelsky Drive, Rockville, MD 20850, USA zkelman@umd.edu.

Abstract

Proliferating cell nuclear antigen (PCNA) forms a trimeric ring that encircles duplex DNA and acts as an anchor for a number of proteins involved in DNA metabolic processes. PCNA has two structurally similar domains (I and II) linked by a long loop (inter-domain connector loop, IDCL) on the outside of each monomer of the trimeric structure that makes up the DNA clamp. All proteins that bind to PCNA do so via a PCNA-interacting peptide (PIP) motif that binds near the IDCL. A small protein, called TIP, binds to PCNA and inhibits PCNA-dependent activities although it does not contain a canonical PIP motif. The X-ray crystal structure of TIP bound to PCNA reveals that TIP binds to the canonical PIP interaction site, but also extends beyond it through a helix that relocates the IDCL. TIP alters the relationship between domains I and II within the PCNA monomer such that the trimeric ring structure is broken, while the individual domains largely retain their native structure. Small angle X-ray scattering (SAXS) confirms the disruption of the PCNA trimer upon addition of the TIP protein in solution and together with the X-ray crystal data, provides a structural basis for the mechanism of PCNA inhibition by TIP.

Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Crystallography, X-Ray
DNA / chemistry*
DNA / metabolism
Nucleic Acid Conformation
Peptides / chemistry*
Peptides / metabolism
Proliferating Cell Nuclear Antigen / chemistry*
Proliferating Cell Nuclear Antigen / metabolism
Protein Binding
Protein Conformation*
Protein Domains
Thermococcus / chemistry
Thermococcus / metabolism

Substances

Peptides
Proliferating Cell Nuclear Antigen
pepBs1-Ac peptide
DNA

Grants and funding

P41 GM111244/GM/NIGMS NIH HHS/United States