1LVC

Crystal structure of the adenylyl cyclase domain of anthrax edema factor (EF) in complex with calmodulin and 2' deoxy, 3' anthraniloyl ATP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Physiological calcium concentrations regulate calmodulin binding and catalysis of adenylyl cyclase exotoxins

Shen, Y., Lee, Y.-S., Soelaiman, S., Bergson, P., Lu, D., Chen, A., Beckingham, K., Grabarek, Z., Mrksich, M., Tang, W.-J.

(2002) EMBO J 21: 6721-6732

  • DOI: 10.1093/emboj/cdf681
  • Primary Citation of Related Structures:  
    1LVC

  • PubMed Abstract: 

    • Edema factor (EF) and CyaA are calmodulin (CaM)-activated adenylyl cyclase exotoxins involved in the pathogenesis of anthrax and whooping cough, respectively. Using spectroscopic, enzyme kinetic and surface plasmon resonance spectroscopy analyses, we ...

    Edema factor (EF) and CyaA are calmodulin (CaM)-activated adenylyl cyclase exotoxins involved in the pathogenesis of anthrax and whooping cough, respectively. Using spectroscopic, enzyme kinetic and surface plasmon resonance spectroscopy analyses, we show that low Ca(2+) concentrations increase the affinity of CaM for EF and CyaA causing their activation, but higher Ca(2+) concentrations directly inhibit catalysis. Both events occur in a physiologically relevant range of Ca(2+) concentrations. Despite the similarity in Ca(2+) sensitivity, EF and CyaA have substantial differences in CaM binding and activation. CyaA has 100-fold higher affinity for CaM than EF. CaM has N- and C-terminal globular domains, each binding two Ca(2+) ions. CyaA can be fully activated by CaM mutants with one defective C-terminal Ca(2+)-binding site or by either terminal domain of CaM while EF cannot. EF consists of a catalytic core and a helical domain, and both are required for CaM activation of EF. Mutations that decrease the interaction of the helical domain with the catalytic core create an enzyme with higher sensitivity to Ca(2+)-CaM activation. However, CyaA is fully activated by CaM without the domain corresponding to the helical domain of EF.

    Related Citations: 
    • Structural basis for the activation of anthrax adenylyl cyclase exotoxin by calmodulin
      Drum, C.L., Yan, S.Z., Bard, J., Shen, Y.Q., Lu, D., Soelaiman, S., Grabarek, Z., Bohm, A., Tang, W.J.
      (2002) Nature 415: 396
    Organizational Affiliation: 

    Ben-May Institute for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
calmodulin-sensitive adenylate cyclaseA, B, C510Bacillus anthracisMutation(s): 0 
Gene Names: cya, pXO1-122, BXA0141, GBAA_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, F149Homo sapiensMutation(s): 0 
Gene Names: CALM1, CALM, CAM, CAM1
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
NIH Common Fund Data Resources
PHAROS  P0DP23
GTEx  ENSG00000198668
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DOT
Query on DOT
Download CCD File 
A, C
3'ANTHRANILOYL-2'-DEOXY-ADENOSINE-5'-TRIPHOSPHATE
C17 H21 N6 O13 P3
FIWKNPONGIOEHC-YNEHKIRRSA-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 %)
DOTKd :  1000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.924α = 90
b = 167.918β = 90
c = 341.743γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Derived calculations