1A26

THE CATALYTIC FRAGMENT OF POLY(ADP-RIBOSE) POLYMERASE COMPLEXED WITH CARBA-NAD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The mechanism of the elongation and branching reaction of poly(ADP-ribose) polymerase as derived from crystal structures and mutagenesis.

Ruf, A.Rolli, V.de Murcia, G.Schulz, G.E.

(1998) J.Mol.Biol. 278: 57-65

  • DOI: 10.1006/jmbi.1998.1673

  • PubMed Abstract: 
  • The binding site for the acceptor substrate poly(ADP-ribose) in the elongation reaction of the ADP-ribosyl transferase poly(ADP-ribose) polymerase (PARP) was detected by cocrystallizing the enzyme with an NAD+ analogue. The site was confirmed by muta ...

    The binding site for the acceptor substrate poly(ADP-ribose) in the elongation reaction of the ADP-ribosyl transferase poly(ADP-ribose) polymerase (PARP) was detected by cocrystallizing the enzyme with an NAD+ analogue. The site was confirmed by mutagenesis studies. In conjunction with the binding site of the donor NAD+, the bound acceptor reveals the geometry of the elongation reaction. It shows in particular that the strictly conserved glutamate residue of all ADP-ribosylating enzymes (Glu988 of PARP) facilitates the reaction by polarizing both, donor and acceptor. Moreover, the binding properties of the acceptor site suggest a mechanism for the branching reaction, that also explains the dual specificity of this transferase for elongation and branching, which is unique among polymer-forming enzymes.


    Related Citations: 
    • Structure of the Catalytic Fragment of Poly(Ad-Ribose) Polymerase from Chicken
      Ruf, A.,Mennissier De Murcia, J.,De Murcia, G.M.,Schulz, G.E.
      (1996) Proc.Natl.Acad.Sci.USA 93: 7481
    • Crystallization and X-Ray Crystallographic Analysis of Recombinant Chicken Poly(Adp-Ribose) Polymerase Catalytic Domain Produced in Sf9 Insect Cells
      Jung, S.,Miranda, E.A.,De Murcia, J.M.,Niedergang, C.,Delarue, M.,Schulz, G.E.,De Murcia, G.M.
      (1994) J.Mol.Biol. 244: 114


    Organizational Affiliation

    Institut für Organische Chemie und Biochemie, Albertstr. 21, Freiburg im Breisgau, D-79104, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
POLY (ADP-RIBOSE) POLYMERASE
A
361Gallus gallusMutation(s): 0 
Gene Names: PARP1 (ADPRT)
EC: 2.4.2.30
Find proteins for P26446 (Gallus gallus)
Go to Gene View: PARP1
Go to UniProtKB:  P26446
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CNA
Query on CNA

Download SDF File 
Download CCD File 
A
CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C22 H30 N7 O13 P2
DGPLSUKWXXSBCU-VGXGLJSLSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.040α = 90.00
b = 64.440β = 90.00
c = 96.720γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1998-01-16 
  • Released Date: 1998-05-27 
  • Deposition Author(s): Ruf, A., Schulz, G.E.

Revision History 

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-07
    Type: Data collection, Other