1S26

Structure of Anthrax Edema Factor-Calmodulin-alpha,beta-methyleneadenosine 5'-triphosphate Complex Reveals an Alternative Mode of ATP Binding to the Catalytic Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of anthrax edema factor-calmodulin-adenosine-5'-(alpha,beta-methylene)-triphosphate complex reveals an alternative mode of ATP binding to the catalytic site

Shen, Y.Guo, Q.Zhukovskaya, N.L.Drum, C.L.Bohm, A.Tang, W.-J.

(2004) Biochem.Biophys.Res.Commun. 317: 309-314

  • DOI: 10.1016/j.bbrc.2004.03.046

  • PubMed Abstract: 
  • Anthrax edema factor (EF) is a key virulence factor secreted by Bacillus anthracis. Here, we report a structure, at 3.0 A resolution, of the catalytic domain of EF (EF3) in complex with calmodulin (CaM) and adenosine 5'-(alpha,beta-methylene)-triphos ...

    Anthrax edema factor (EF) is a key virulence factor secreted by Bacillus anthracis. Here, we report a structure, at 3.0 A resolution, of the catalytic domain of EF (EF3) in complex with calmodulin (CaM) and adenosine 5'-(alpha,beta-methylene)-triphosphate (AMPCPP). Although the binding of the triphosphate of AMPCPP to EF3 can be superimposed on that of previously determined 3'deoxy-ATP (3'dATP) and 2'deoxy 3' anthraniloyl-ATP (2'd3' ANT-ATP) in EF3-CaM, the ribose and the adenine rings of AMPCPP are rotated approximately 105 and 180 degrees, respectively, relative to those of 3'dATP and 2'd3'ANT-ATP. Based on this model, K382 and F586 should play key roles in the recognition of adenine. However, mutations of these residues to alanine either separately or together cause only modest changes in Michaelis-Menten constants and IC50 values of AMPCPP and cAMP. Therefore, this alternate binding mode of the adenosine of AMPCPP binds to EF likely playing only a minor role in ATP binding and in catalysis.


    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, 924 East 57th Street, Chicago, IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calmodulin-sensitive adenylate cyclase
A, B, C
510Bacillus anthracisMutation(s): 0 
Gene Names: cya
EC: 4.6.1.1
Find proteins for P40136 (Bacillus anthracis)
Go to UniProtKB:  P40136
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calmodulin
D, E, F
148Homo sapiensMutation(s): 0 
Gene Names: CALM2 (CAM2, CAMB)
Find proteins for P0DP24 (Homo sapiens)
Go to Gene View: CALM2
Go to UniProtKB:  P0DP24
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
YB
Query on YB

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

Download SDF File 
Download CCD File 
D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
APC
Query on APC

Download SDF File 
Download CCD File 
A, B, C
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
APCKi: 850000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.264 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 117.555α = 90.00
b = 167.605β = 90.00
c = 345.346γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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