1XFX

Crystal structure of anthrax edema factor (EF) in complex with calmodulin in the presence of 10 millimolar exogenously added calcium chloride


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.262 

wwPDB Validation   3D Report Full Report


This is version 1.3 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.Florian, J.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, 1Y0V

  • 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. CaM has N- and C-terminal domains and each domain can bind two calcium ions ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin-sensitive adenylate cyclase
A, B, C, D, E, F
A, B, C, D, E, F
777Bacillus anthracisMutation(s): 0 
Gene Names: cyapXO1-122BXA0141GBAA_pXO1_0142
EC: 4.6.1.1
UniProt
Find proteins for P40136 (Bacillus anthracis)
Explore P40136 
Go to UniProtKB:  P40136
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40136
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin 2149Homo sapiensMutation(s): 10 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DP23
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth Q],
BA [auth Q],
CA [auth Q],
DA [auth Q],
EA [auth R],
AA [auth Q],
BA [auth Q],
CA [auth Q],
DA [auth Q],
EA [auth R],
FA [auth R],
GA [auth R],
HA [auth R],
IA [auth S],
JA [auth S],
KA [auth S],
LA [auth S],
MA [auth T],
NA [auth T],
OA [auth T],
PA [auth T],
S [auth O],
T [auth O],
U [auth O],
V [auth O],
W [auth P],
X [auth P],
Y [auth P],
Z [auth P]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
G [auth O],
H [auth P],
I [auth Q],
J [auth R],
K [auth S],
G [auth O],
H [auth P],
I [auth Q],
J [auth R],
K [auth S],
L [auth T]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.262 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 318.303α = 90
b = 183.765β = 90.02
c = 141.516γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-12-20
    Changes: Database references