1PK0

Crystal Structure of the EF3-CaM complexed with PMEApp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Selective inhibition of anthrax edema factor by adefovir, a drug for chronic hepatitis B virus infection.

Shen, Y.Zhukovskaya, N.L.Zimmer, M.I.Soelaiman, S.Bergson, P.Wang, C.R.Gibbs, C.S.Tang, W.J.

(2004) Proc Natl Acad Sci U S A 101: 3242-3247

  • DOI: 10.1073/pnas.0306552101
  • Primary Citation of Related Structures:  
    1PK0

  • PubMed Abstract: 
  • Edema factor (EF), a key virulence factor in anthrax pathogenesis, has calmodulin (CaM)-activated adenylyl cyclase activity. We have found that adefovir dipivoxil, a drug approved to treat chronic infection of hepatitis B virus, effectively inhibits ...

    Edema factor (EF), a key virulence factor in anthrax pathogenesis, has calmodulin (CaM)-activated adenylyl cyclase activity. We have found that adefovir dipivoxil, a drug approved to treat chronic infection of hepatitis B virus, effectively inhibits EF-induced cAMP accumulation and changes in cytokine production in mouse primary macrophages. Adefovir diphosphate (PMEApp), the active cellular metabolite of adefovir dipivoxil, inhibits the adenylyl cyclase activity of EF in vitro with high affinity (K(i) = 27 nM). A crystal structure of EF-CaM-PMEApp reveals that the catalytic site of EF forms better van der Waals contacts and more hydrogen bonds with PMEApp than with its endogenous substrate, ATP, providing an explanation for the approximately 10,000-fold higher affinity EF-CaM has for PMEApp versus ATP. Adefovir dipivoxil is a clinically approved drug that can block the action of an anthrax toxin. It can be used to address the role of EF in anthrax pathogenesis.


    Related Citations: 
    • Physiological calcium concentrations regulate calmodulin binding and catalysis of adenylyl cyclase exotoxins
      Shen, Y.-Q., Lee, Y.-S., Soelaiman, S., Bergson, P., Lu, D., Chen, A., Beckingham, K., Grabarek, Z., Mrksich, M., Tang, W.-J.
      (2002) EMBO J 21: 6721

    Organizational Affiliation

    Ben-May Institute for Cancer Research, University of Chicago, 924 East 57th Street, Chicago, IL 60637, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin-sensitive adenylate cyclaseA, B, C507Bacillus anthracisMutation(s): 0 
Gene Names: CYA OR PXO1-122cyapXO1-122BXA0141GBAA_pXO1_0142
EC: 4.6.1.1
Find proteins for P40136 (Bacillus anthracis)
Explore P40136 
Go to UniProtKB:  P40136
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CalmodulinD, E, F147Homo sapiensMutation(s): 0 
Gene Names: (CALM1 OR CAM1 OR CALM OR CAM)CALM1CALMCAMCAM1
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
NIH Common Fund Data Resources
PHAROS  P0DP23
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EMA
Query on EMA

Download CCD File 
A, B, C
(ADENIN-9-YL-ETHOXYMETHYL)-HYDROXYPHOSPHINYL-DIPHOSPHATE
C8 H14 N5 O10 P3
MELHEUHXJKQZNC-UHFFFAOYSA-N
 Ligand Interaction
YB
Query on YB

Download CCD File 
A, B, C
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EMAKi :  27   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.264 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.263α = 90
b = 165.759β = 90
c = 342.409γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2003-06-04 
  • Released Date: 2004-02-10 
  • Deposition Author(s): Shen, Y., Tang, W.J.

Revision History 

  • Version 1.0: 2004-02-10
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Derived calculations