5LW0

Oryza sativa APL macrodomain in complex with ADP-ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

The role of ADP-ribosylation in regulating DNA interstrand crosslink repair.

Gunn, A.R.Banos-Pinero, B.Paschke, P.Sanchez-Pulido, L.Ariza, A.Day, J.Emrich, M.Leys, D.Ponting, C.P.Ahel, I.Lakin, N.D.

(2016) J Cell Sci 129: 3845-3858

  • DOI: https://doi.org/10.1242/jcs.193375
  • Primary Citation of Related Structures:  
    5LW0, 5LW6

  • PubMed Abstract: 

    ADP-ribosylation by ADP-ribosyltransferases (ARTs) has a well-established role in DNA strand break repair by promoting enrichment of repair factors at damage sites through ADP-ribose interaction domains. Here, we exploit the simple eukaryote Dictyostelium to uncover a role for ADP-ribosylation in regulating DNA interstrand crosslink repair and redundancy of this pathway with non-homologous end-joining (NHEJ). In silico searches were used to identify a protein that contains a permutated macrodomain (which we call aprataxin/APLF-and-PNKP-like protein; APL). Structural analysis reveals that this permutated macrodomain retains features associated with ADP-ribose interactions and that APL is capable of binding poly(ADP-ribose) through this macrodomain. APL is enriched in chromatin in response to cisplatin treatment, an agent that induces DNA interstrand crosslinks (ICLs). This is dependent on the macrodomain of APL and the ART Adprt2, indicating a role for ADP-ribosylation in the cellular response to cisplatin. Although adprt2 - cells are sensitive to cisplatin, ADP-ribosylation is evident in these cells owing to redundant signalling by the double-strand break (DSB)-responsive ART Adprt1a, promoting NHEJ-mediated repair. These data implicate ADP-ribosylation in DNA ICL repair and identify that NHEJ can function to resolve this form of DNA damage in the absence of Adprt2.


  • Organizational Affiliation

    Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Basic helix-loop-helix, putative, expressed
A, B
231Oryza sativa Japonica GroupMutation(s): 0 
Gene Names: LOC_Os03g18210
UniProt
Find proteins for B8ALM5 (Oryza sativa subsp. indica)
Explore B8ALM5 
Go to UniProtKB:  B8ALM5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8ALM5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AR6
Query on AR6

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-ZQSHOCFMSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
G [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GLY
Query on GLY

Download Ideal Coordinates CCD File 
H [auth B],
I [auth B]
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.496α = 90
b = 91.318β = 103.32
c = 62.882γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2016-10-26 
  • Deposition Author(s): Ariza, A.

Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomC1521/A12353
Medical Research Council (United Kingdom)United KingdomMR/L000164/1
NC3RsUnited KingdomNC/K00137X/1
Wellcome TrustUnited Kingdom101794
European Research CouncilUnited Kingdom281739

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 2.0: 2017-09-13
    Changes: Atomic model, Author supporting evidence
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary