5BNF

Apo structure of porcine CD38


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.207 

wwPDB Validation   3D Report Full Report


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Literature

Porcine CD38 exhibits prominent secondary NAD(+) cyclase activity.

Ting, K.Y.Leung, C.F.Graeff, R.M.Lee, H.C.Hao, Q.Kotaka, M.

(2016) Protein Sci 25: 650-661

  • DOI: https://doi.org/10.1002/pro.2859
  • Primary Citation of Related Structures:  
    5BNF, 5BNI

  • PubMed Abstract: 

    Cyclic ADP-ribose (cADPR) mobilizes intracellular Ca(2+) stores and activates Ca(2+) influx to regulate a wide range of physiological processes. It is one of the products produced from the catalysis of NAD(+) by the multifunctional CD38/ADP-ribosyl cyclase superfamily. After elimination of the nicotinamide ring by the enzyme, the reaction intermediate of NAD(+) can either be hydrolyzed to form linear ADPR or cyclized to form cADPR. We have previously shown that human CD38 exhibits a higher preference towards the hydrolysis of NAD(+) to form linear ADPR while Aplysia ADP-ribosyl cyclase prefers cyclizing NAD(+) to form cADPR. In this study, we characterized the enzymatic properties of porcine CD38 and revealed that it has a prominent secondary NAD(+) cyclase activity producing cADPR. We also determined the X-ray crystallographic structures of porcine CD38 and were able to observe conformational flexibility at the base of the active site of the enzyme which allow the NAD(+) reaction intermediate to adopt conformations resulting in both hydrolysis and cyclization forming linear ADPR and cADPR respectively.


  • Organizational Affiliation

    School of Life Sciences, the Chinese University of Hong Kong, Hong Kong.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
A, B
232Sus scrofaMutation(s): 0 
Gene Names: CD38
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.541α = 90
b = 103.856β = 90
c = 63.689γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Hong Kong--

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release