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: 2.2 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 

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:  

  • 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 role ...

    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

    the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden and.,From the Structural Genomics Consortium and the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden and.,From the Structural Genomics Consortium and the Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden and herwig.schuler@ki.se.,the Department of Chemistry, Umeå University, 90187 Umeå, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly [ADP-ribose] polymerase 12
A, B, C, D, E, F
198Homo sapiensMutation(s): 0 
Gene Names: PARP12 (ZC3HDC1)
EC: 2.4.2.-
Find proteins for Q9H0J9 (Homo sapiens)
Go to Gene View: PARP12
Go to UniProtKB:  Q9H0J9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
GAB
Query on GAB

Download SDF File 
Download CCD File 
A, B, C, D, E, F
3-AMINOBENZOIC ACID
GABACULINE
C7 H7 N O2
XFDUHJPVQKIXHO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.198 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 206.590α = 90.00
b = 206.590β = 90.00
c = 84.730γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
SOLVEphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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