Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


ADP-ribosyl cyclase; crystal structures reveal a covalent intermediate.

Love, M.L.Szebenyi, D.M.Kriksunov, I.A.Thiel, D.J.Munshi, C.Graeff, R.Lee, H.C.Hao, Q.

(2004) Structure 12: 477-486

  • DOI: https://doi.org/10.1016/j.str.2004.02.006
  • Primary Citation of Related Structures:  
    1R0S, 1R12, 1R15, 1R16

  • PubMed Abstract: 

    ADP-ribosyl cyclase catalyzes the elimination of nicotinamide from NAD and cyclization to cADPR, a known second messenger in cellular calcium signaling pathways. We have determined to 2.0 A resolution the structure of Aplysia cyclase with ribose-5-phosphate bound covalently at C3' and with the base exchange substrate (BES), pyridylcarbinol, bound to the active site. In addition, further refinement at 2.4 A resolution of the structure of nicotinamide-bound cyclase, which was previously reported, reveals that ribose-5-phosphate is also covalently bound in this structure, and a second nicotinamide site was identified. The structures of native and mutant Glu179Ala cyclase were also solved to 1.7 and 2.0 A respectively. It is proposed that the second nicotinamide site serves to promote cyclization by clearing the active site of the nicotinamide byproduct. Moreover, a ribosylation mechanism can be proposed in which the cyclization reaction proceeds through a covalently bound intermediate.

  • Organizational Affiliation

    Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosyl cyclase
A, B, C, D, E
A, B, C, D, E, F, G, H
258Aplysia californicaMutation(s): 0 
Find proteins for P29241 (Aplysia californica)
Explore P29241 
Go to UniProtKB:  P29241
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29241
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on N

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth H]
I [auth A]
L [auth B]
O [auth C]
AA [auth G],
DA [auth H],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
C5 H11 O7 P
Query on NCA

Download Ideal Coordinates CCD File 
BA [auth G]
CA [auth G]
EA [auth H]
FA [auth H]
J [auth A]
BA [auth G],
CA [auth G],
EA [auth H],
FA [auth H],
J [auth A],
K [auth A],
M [auth B],
N [auth B],
P [auth C],
Q [auth C],
S [auth D],
T [auth D],
V [auth E],
W [auth E],
Y [auth F],
Z [auth F]
C6 H6 N2 O
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.4α = 88.16
b = 75.32β = 89.22
c = 138.13γ = 89.09
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-03-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance