5MAV

Crystal structure of human PCNA in complex with PARG (poly(ADP-ribose) glycohydrolase) peptide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A novel non-canonical PIP-box mediates PARG interaction with PCNA.

Kaufmann, T.Grishkovskaya, I.Polyansky, A.A.Kostrhon, S.Kukolj, E.Olek, K.M.Herbert, S.Beltzung, E.Mechtler, K.Peterbauer, T.Gotzmann, J.Zhang, L.Hartl, M.Zagrovic, B.Elsayad, K.Djinovic-Carugo, K.Slade, D.

(2017) Nucleic Acids Res 45: 9741-9759

  • DOI: 10.1093/nar/gkx604
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Poly(ADP-ribose) glycohydrolase (PARG) regulates cellular poly(ADP-ribose) (PAR) levels by rapidly cleaving glycosidic bonds between ADP-ribose units. PARG interacts with proliferating cell nuclear antigen (PCNA) and is strongly recruited to DNA dama ...

    Poly(ADP-ribose) glycohydrolase (PARG) regulates cellular poly(ADP-ribose) (PAR) levels by rapidly cleaving glycosidic bonds between ADP-ribose units. PARG interacts with proliferating cell nuclear antigen (PCNA) and is strongly recruited to DNA damage sites in a PAR- and PCNA-dependent fashion. Here we identified PARG acetylation site K409 that is essential for its interaction with PCNA, its localization within replication foci and its recruitment to DNA damage sites. We found K409 to be part of a non-canonical PIP-box within the PARG disordered regulatory region. The previously identified putative N-terminal PIP-box does not bind PCNA directly but contributes to PARG localization within replication foci. X-ray structure and MD simulations reveal that the PARG non-canonical PIP-box binds PCNA in a manner similar to other canonical PIP-boxes and may represent a new type of PIP-box. While the binding of previously described PIP-boxes is based on hydrophobic interactions, PARG PIP-box binds PCNA via both stabilizing hydrophobic and fine-tuning electrostatic interactions. Our data explain the mechanism of PARG-PCNA interaction through a new PARG PIP-box that exhibits non-canonical sequence properties but a canonical mode of PCNA binding.


    Organizational Affiliation

    Department of Biochemistry, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, 1030 Vienna, Austria.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proliferating cell nuclear antigen
A, B, C, D, E, F
264Homo sapiensMutation(s): 0 
Gene Names: PCNA
Find proteins for P12004 (Homo sapiens)
Go to UniProtKB:  P12004
NIH Common Fund Data Resources
PHAROS  P12004
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Poly (ADP-ribose) glycohydrolase
G, H, K, L, M, N
19Homo sapiensMutation(s): 0 
Gene Names: PARG
Find proteins for Q0MQR4 (Homo sapiens)
Go to UniProtKB:  Q0MQR4
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.597α = 90
b = 153.604β = 96.9
c = 85.512γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-02
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection