1Y0V

Crystal structure of anthrax edema factor (EF) in complex with calmodulin and pyrophosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.286 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Calcium-independent calmodulin binding and two-metal-ion catalytic mechanism of anthrax edema factor

Shen, Y.Zhukovskaya, N.L.Guo, Q.Tang, W.-J.

(2005) Embo J. 24: 929-941

  • DOI: 10.1038/sj.emboj.7600574
  • Primary Citation of Related Structures:  1XFU, 1XFV, 1XFW, 1XFX, 1XFY, 1XFZ

  • PubMed Abstract: 
  • Edema factor (EF), a key anthrax exotoxin, has an anthrax protective antigen-binding domain (PABD) and a calmodulin (CaM)-activated adenylyl cyclase domain. Here, we report the crystal structures of CaM-bound EF, revealing the architecture of EF PABD ...

    Edema factor (EF), a key anthrax exotoxin, has an anthrax protective antigen-binding domain (PABD) and a calmodulin (CaM)-activated adenylyl cyclase domain. Here, we report the crystal structures of CaM-bound EF, revealing the architecture of EF PABD. CaM has N- and C-terminal domains and each domain can bind two calcium ions. Calcium binding induces the conformational change of CaM from closed to open. Structures of the EF-CaM complex show how EF locks the N-terminal domain of CaM into a closed conformation regardless of its calcium-loading state. This represents a mechanism of how CaM effector alters the calcium affinity of CaM and uncouples the conformational change of CaM from calcium loading. Furthermore, structures of EF-CaM complexed with nucleotides show that EF uses two-metal-ion catalysis, a prevalent mechanism in DNA and RNA polymerases. A histidine (H351) further facilitates the catalysis of EF by activating a water to deprotonate 3'OH of ATP. Mammalian adenylyl cyclases share no structural similarity with EF and they also use two-metal-ion catalysis, suggesting the catalytic mechanism-driven convergent evolution of two structurally diverse adenylyl cyclases.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calmodulin-sensitive adenylate cyclase
A, B, C, D, E, F
777Bacillus anthracisGene Names: cya
EC: 4.6.1.1
Find proteins for P40136 (Bacillus anthracis)
Go to UniProtKB:  P40136
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calmodulin
H, I, J, K, L, M
146Xenopus laevisGene Names: calm2-b
Find proteins for P0DP35 (Xenopus laevis)
Go to UniProtKB:  P0DP35
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
H, I, J, K, L, M
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.286 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 317.509α = 90.00
b = 183.348β = 90.05
c = 141.812γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
CNSphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance