3DZG

Crystal structure of human CD38 extracellular domain, ara-F-ribose-5'-phosphate/nicotinamide complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Literature

Covalent and Noncovalent Intermediates of an NAD Utilizing Enzyme, Human CD38.

Liu, Q.Kriksunov, I.A.Jiang, H.Graeff, R.Lin, H.Lee, H.C.Hao, Q.

(2008) Chem Biol 15: 1068-1078

  • DOI: https://doi.org/10.1016/j.chembiol.2008.08.007
  • Primary Citation of Related Structures:  
    3DZF, 3DZG, 3DZH, 3DZI, 3DZJ, 3DZK

  • PubMed Abstract: 

    Enzymatic utilization of nicotinamide adenine dinucleotide (NAD) has increasingly been shown to have fundamental roles in gene regulation, signal transduction, and protein modification. Many of the processes require the cleavage of the nicotinamide moiety from the substrate and the formation of a reactive intermediate. Using X-ray crystallography, we show that human CD38, an NAD-utilizing enzyme, is capable of catalyzing the cleavage reactions through both covalent and noncovalent intermediates, depending on the substrate used. The covalent intermediate is resistant to further attack by nucleophiles, resulting in mechanism-based enzyme inactivation. The noncovalent intermediate is stabilized mainly through H-bond interactions, but appears to remain reactive. Our structural results favor the proposal of a noncovalent intermediate during normal enzymatic utilization of NAD by human CD38 and provide structural insights into the design of covalent and noncovalent inhibitors targeting NAD-utilization pathways.


  • Organizational Affiliation

    MacCHESS, Cornell High Energy Synchrotron Source, Department of Chemistry and Chemical Biology, School of Applied & Engineering Physics, Cornell University, Ithaca, NY 14853, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosyl cyclase 1
A, B
262Homo sapiensMutation(s): 5 
Gene Names: CD38
EC: 3.2.2.5 (PDB Primary Data), 3.2.2 (UniProt), 3.2.2.6 (UniProt), 2.4.99.20 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P28907 (Homo sapiens)
Explore P28907 
Go to UniProtKB:  P28907
PHAROS:  P28907
GTEx:  ENSG00000004468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28907
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.689α = 106.06
b = 52.812β = 91.95
c = 65.381γ = 95.12
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-11-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2016-06-08
    Changes: Non-polymer description
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2021-10-20
    Changes: Database references, Structure summary
  • Version 1.5: 2023-08-30
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-11-20
    Changes: Structure summary