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 
  • R-Value Observed: 0.168 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    1A26

  • 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 mutagenesis studies ...

    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 U S A 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POLY (ADP-RIBOSE) POLYMERASEA361Gallus gallusMutation(s): 0 
Gene Names: PARP1ADPRT
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt
Find proteins for P26446 (Gallus gallus)
Explore P26446 
Go to UniProtKB:  P26446
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26446
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CNA
Query on CNA

Download Ideal Coordinates CCD File 
B [auth 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 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.04α = 90
b = 64.44β = 90
c = 96.72γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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