3I9O

Crystal structure of ADP ribosyl cyclase complexed with ribo-2'F-ADP ribose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

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This is version 1.2 of the entry. See complete history


Literature

Mechanism of cyclizing NAD to cyclic ADP-ribose by ADP-ribosyl cyclase and CD38

Graeff, R.Liu, Q.Kriksunov, I.A.Kotaka, M.Oppenheimer, N.Hao, Q.Lee, H.C.

(2009) J Biol Chem 284: 27629-27636

  • DOI: https://doi.org/10.1074/jbc.M109.030965
  • Primary Citation of Related Structures:  
    3I9O

  • PubMed Abstract: 

    Mammalian CD38 and its Aplysia homolog, ADP-ribosyl cyclase (cyclase), are two prominent enzymes that catalyze the synthesis and hydrolysis of cyclic ADP-ribose (cADPR), a Ca(2+) messenger molecule responsible for regulating a wide range of cellular functions. Although both use NAD as a substrate, the cyclase produces cADPR, whereas CD38 produces mainly ADP-ribose (ADPR). To elucidate the catalytic differences and the mechanism of cyclizing NAD, the crystal structure of a stable complex of the cyclase with an NAD analog, ribosyl-2'F-2'deoxynicotinamide adenine dinucleotide (ribo-2'-F-NAD), was determined. The results show that the analog was a substrate of the cyclase and that during the reaction, the nicotinamide group was released and a stable intermediate was formed. The terminal ribosyl unit at one end of the intermediate formed a close linkage with the catalytic residue (Glu-179), whereas the adenine ring at the other end stacked closely with Phe-174, suggesting that the latter residue is likely to be responsible for folding the linear substrate so that the two ends can be cyclized. Mutating Phe-174 indeed reduced cADPR production but enhanced ADPR production, converting the cyclase to be more CD38-like. Changing the equivalent residue in CD38, Thr-221 to Phe, correspondingly enhanced cADPR production, and the double mutation, Thr-221 to Phe and Glu-146 to Ala, effectively converted CD38 to a cyclase. This study provides the first detailed evidence of the cyclization process and demonstrates the feasibility of engineering the reactivity of the enzymes by mutation, setting the stage for the development of tools to manipulate cADPR metabolism in vivo.


  • Organizational Affiliation

    Department of Physiology, University of Minnesota, Minneapolis, Minnesota 55455, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosyl cyclase
A, B
258Aplysia californicaMutation(s): 0 
EC: 3.2.2.5
UniProt
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
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AVW
Query on AVW

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4S)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate
C15 H22 F N5 O12 P2
GOCJJDZHXMDJEZ-AOOZFPJJSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.726α = 90
b = 56.726β = 90
c = 360.333γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary