2PQF

Human Poly(ADP-Ribose) Polymerase 12, Catalytic fragment in complex with an inhibitor 3-Aminobenzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Basis for Lack of ADP-ribosyltransferase Activity in Poly(ADP-ribose) Polymerase-13/Zinc Finger Antiviral Protein.

Karlberg, T.Klepsch, M.Thorsell, A.G.Andersson, C.D.Linusson, A.Schuler, H.

(2015) J Biol Chem 290: 7336-7344

  • DOI: 10.1074/jbc.M114.630160
  • Primary Citation of Related Structures:  
    2X5Y, 4X52, 3GEY, 3BLJ, 2PQF

  • PubMed Abstract: 
  • The mammalian poly(ADP-ribose) polymerase (PARP) family includes ADP-ribosyltransferases with diphtheria toxin homology (ARTD). Most members have mono-ADP-ribosyltransferase activity. PARP13/ARTD13, also called zinc finger antiviral protein, has roles in viral immunity and microRNA-mediated stress responses ...

    The mammalian poly(ADP-ribose) polymerase (PARP) family includes ADP-ribosyltransferases with diphtheria toxin homology (ARTD). Most members have mono-ADP-ribosyltransferase activity. PARP13/ARTD13, also called zinc finger antiviral protein, has roles in viral immunity and microRNA-mediated stress responses. PARP13 features a divergent PARP homology domain missing a PARP consensus sequence motif; the domain has enigmatic functions and apparently lacks catalytic activity. We used x-ray crystallography, molecular dynamics simulations, and biochemical analyses to investigate the structural requirements for ADP-ribosyltransferase activity in human PARP13 and two of its functional partners in stress granules: PARP12/ARTD12, and PARP15/BAL3/ARTD7. The crystal structure of the PARP homology domain of PARP13 shows obstruction of the canonical active site, precluding NAD(+) binding. Molecular dynamics simulations indicate that this closed cleft conformation is maintained in solution. Introducing consensus side chains in PARP13 did not result in 3-aminobenzamide binding, but in further closure of the site. Three-dimensional alignment of the PARP homology domains of PARP13, PARP12, and PARP15 illustrates placement of PARP13 residues that deviate from the PARP family consensus. Introducing either one of two of these side chains into the corresponding positions in PARP15 abolished PARP15 ADP-ribosyltransferase activity. Taken together, our results show that PARP13 lacks the structural requirements for ADP-ribosyltransferase activity.


    Organizational Affiliation

    From the Structural Genomics Consortium and the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden and herwig.schuler@ki.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 12A, B, C, D, E, F198Homo sapiensMutation(s): 2 
Gene Names: PARP12ZC3HDC1
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
Find proteins for Q9H0J9 (Homo sapiens)
Explore Q9H0J9 
Go to UniProtKB:  Q9H0J9
NIH Common Fund Data Resources
PHAROS:  Q9H0J9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.59α = 90
b = 206.59β = 90
c = 84.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2015-02-04
    Changes: Database references
  • Version 1.4: 2015-04-22
    Changes: Database references