1R16

Aplysia ADP ribosyl cyclase with bound pyridylcarbinol and R5P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1016/j.str.2004.02.006
  • Primary Citation of Related Structures:  

  • 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-ph ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosyl cyclase
A, B
258Aplysia californicaMutation(s): 0 
EC: 3.2.2.6
Find proteins for P29241 (Aplysia californica)
Go to UniProtKB:  P29241
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
N
Query on N

Download SDF File 
Download CCD File 
A, B
ANY 5'-MONOPHOSPHATE NUCLEOTIDE
1-DEOXY-RIBOFURANOSE-5'-PHOSPHATE
C5 H11 O7 P
CYZZKTRFOOKUMT-LMVFSUKVSA-N
 Ligand Interaction
PYF
Query on PYF

Download SDF File 
Download CCD File 
A, B
3-PYRIDINYLCARBINOL
PYRIDIN-3-YLMETHANOL
C6 H7 N O
MVQVNTPHUGQQHK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.212 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.293α = 90.00
b = 58.349β = 100.70
c = 72.368γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
CNSrefinement
CCP4data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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