9IFV | pdb_00009ifv

PARP15 catalytic domain mutant (R576E) in complex with 3-aminobenzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Regulation of ADP-ribosyltransferase activity by ART domain dimerization in PARP15.

Ebenwaldner, C.Garcia Saura, A.G.Ekstrom, S.Bernfur, K.Moche, M.Logan, D.T.Cohen, M.S.Schuler, H.

(2025) Nat Commun 16: 9567-9567

  • DOI: https://doi.org/10.1038/s41467-025-65315-9
  • Primary Citation of Related Structures:  
    9IFV

  • PubMed Abstract: 

    PARP15 is a mono-ADP-ribosyltransferase that targets an unknown set of proteins as well as RNA. Its evolutionary relationship with PARP14 suggests roles in antiviral defence; its localization to stress granules points to functions in the regulation of translation. Here we show that the transferase domain of PARP15 dimerizes in solution; the formation of dimers is a prerequisite for catalytic activity and monomeric mutant variants of the domain are inactive. In cells, dimer-disrupting mutations abrogate catalytic activity and alter the subcellular localization of the full-length protein. Using biophysical methods, including X-ray crystallography and HDX-MS, we provide evidence for a regulatory mechanism by which dimerization enables correct target engagement rather than NAD + co-substrate binding, and by which the two protomers of the dimer operate independently of one another. Together, our results uncover a regulatory mechanism in a PARP family enzyme.


  • Organizational Affiliation
    • Division of Biochemistry and Structural Biology, Department of Chemistry, Lund University, Lund, Sweden.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein mono-ADP-ribosyltransferase PARP15
A, B
221Homo sapiensMutation(s): 1 
Gene Names: PARP15BAL3
EC: 2.4.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q460N3 (Homo sapiens)
Explore Q460N3 
Go to UniProtKB:  Q460N3
PHAROS:  Q460N3
GTEx:  ENSG00000173200 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ460N3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.713α = 90
b = 76.697β = 90
c = 155.562γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
Aimlessdata scaling
autoPROCdata processing
autoPROCdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
CancerfondenSweden23-3027Pj

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references