Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 59.16 kDa 
• Atom Count: 4300 
• Modelled Residue Count: 502 
• Deposited Residue Count: 516 
• Unique protein chains: 1

1R12

Native Aplysia ADP ribosyl cyclase

• PDB DOI: 10.2210/pdb1R12/pdb

• Classification: HYDROLASE
• Organism(s): Aplysia californica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-09-23 Released: 2004-03-09 
• Deposition Author(s): Love, M.L., Szebenyi, D.M.E., Kriksunov, I.A., Thiel, D.J., Munshi, C., Graeff, R., Lee, H.C., Hao, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.238 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 

Literature

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

• PubMed: 15016363 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-ribosyl cyclase	A, B	258	Aplysia californica	Mutation(s): 0  EC: 3.2.2.5 (PDB Primary Data), 3.2.2.6 (UniProt), 2.4.99.20 (UniProt)
UniProt
Find proteins for P29241 (Aplysia californica) Explore P29241  Go to UniProtKB:  P29241

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.238 
• R-Value Work: 0.208 
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.856	α = 90
b = 58.503	β = 100.8
c = 71.603	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-09-23 
• Released Date: 2004-03-09 
Deposition Author(s): Love, M.L., Szebenyi, D.M.E., Kriksunov, I.A., Thiel, D.J., Munshi, C., Graeff, R., Lee, H.C., Hao, Q.

Revision History  

• 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