5BNI

Porcine CD38 complexed with complexed with a covalent intermediate, ribo-F-ribose-5'-phosphate

• PDB DOI: https://doi.org/10.2210/pdb5BNI/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2015-05-26 Released: 2016-05-25 
• Deposition Author(s): Ting, K.Y., Leung, C.F.P., Graeff, R.M., Lee, H.C., Hao, Q., Kotaka, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

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

• PubMed: 26660500 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53.41 kDa 
• Atom Count: 3,875 
• Modelled Residue Count: 463 
• Deposited Residue Count: 464 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	232	Sus scrofa	Mutation(s): 0  Gene Names: CD38

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AVW	C [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: 2.50 Å
• R-Value Free:  0.278 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.507	α = 90
b = 104.973	β = 90
c = 63.785	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Ting, K.Y., Leung, C.F.P., Graeff, R.M., Lee, H.C., Hao, Q., Kotaka, M.

Revision History  

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