5BNI | pdb_00005bni

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), 0.278 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.186 (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 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.
The Centre of Novel Biomaterials, the Chinese University of Hong Kong, Hong Kong.
School of Chinese Medicine, Hong Kong Baptist University, Hong Kong.
Department of Physiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong.
School of Chemical Biology & Biotechnology, Peking University Campus, Shenzhen, China.

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 
• Modeled 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), 0.278 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.186 (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
  
• Version 1.1: 2025-04-09
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2025-09-17
  Changes: Advisory, Derived calculations, Structure summary