3F6Y

Conformational Closure of the Catalytic Site of Human CD38 Induced by Calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformational Closure of the Catalytic Site of Human CD38 Induced by Calcium

Liu, Q.Graeff, R.Kriksunov, I.A.Lam, C.M.C.Lee, H.C.Hao, Q.

(2008) Biochemistry 47: 13966-13973


  • PubMed Abstract: 
  • First identified on the surface of lymphoids as a type II transmembrane protein, CD38 has now been established to have dual functions not only as a receptor but also as a multifunctional enzyme,catalyzing the synthesis of and hydrolysis of a general ...

    First identified on the surface of lymphoids as a type II transmembrane protein, CD38 has now been established to have dual functions not only as a receptor but also as a multifunctional enzyme,catalyzing the synthesis of and hydrolysis of a general calcium messenger molecule, cyclic ADP-ribose(cADPR). The receptorial functions of CD38 include the induction of cell adhesion, differentiation,apoptosis, and cytokine production upon antibody ligation. Here we determined the crystal structure of calcium-loaded human CD38 at 1.45 A resolution which reveals that CD38 undergoes dramatic structural changes to an inhibited conformation in the presence of calcium. The structural changes are highly localized and occur in only two regions. The first region is part of the active site and consists of residues 121-141.In the presence of calcium, W125 moves 5 A into the active site and forms hydrophobic interactions with W189. The movement closes the active site pocket and reduces entry of substrates, resulting in inhibition of the enzymatic activity. The structural role of calcium in inducing these conformational changes is readily visualized in the crystal structure. The other region that undergoes calcium-induced changes is at the receptor region, where a highly ordered helix is unraveled to a random coil. The results suggest a novel conformational coupling mechanism, whereby protein interaction targeted at the receptor region can effectively regulate the enzymatic activity of CD38.


    Organizational Affiliation

    MacCHESS, Cornell High Energy Synchrotron Source, and School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADP-ribosyl cyclase 1
A
262Homo sapiensMutation(s): 6 
Gene Names: CD38
EC: 3.2.2.6
Find proteins for P28907 (Homo sapiens)
Go to Gene View: CD38
Go to UniProtKB:  P28907
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.146 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.687α = 90.00
b = 60.058β = 129.69
c = 56.932γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-11-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance