1XFV

Crystal structure of anthrax edema factor (EF) in complex with calmodulin and 3' deoxy-ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 

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Ligand Structure Quality Assessment 


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, Q.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:  
    1XFV, 1XFU, 1XFZ, 1XFY, 1XFX, 1XFW, 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin-sensitive adenylate cyclaseA, B, C, D, E, F777Bacillus 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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Calmodulin 2G [auth O], H [auth P], I [auth Q], J [auth R], K [auth S], L [auth T]149Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3AT (Subject of Investigation/LOI)
Query on 3AT

Download Ideal Coordinates CCD File 
AA [auth E], DA [auth F], O [auth A], R [auth B], U [auth C], X [auth D]3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
NLIHPCYXRYQPSD-BAJZRUMYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
EA [auth O] , FA [auth O] , GA [auth O] , HA [auth P] , IA [auth P] , JA [auth P] , KA [auth Q] , LA [auth Q] , 
EA [auth O],  FA [auth O],  GA [auth O],  HA [auth P],  IA [auth P],  JA [auth P],  KA [auth Q],  LA [auth Q],  MA [auth Q],  NA [auth R],  OA [auth R],  PA [auth R],  QA [auth S],  RA [auth S],  SA [auth S],  TA [auth T],  UA [auth T],  VA [auth T]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth F] , CA [auth F] , M [auth A] , N [auth A] , P [auth B] , Q [auth B] , S [auth C] , T [auth C] , 
BA [auth F],  CA [auth F],  M [auth A],  N [auth A],  P [auth B],  Q [auth B],  S [auth C],  T [auth C],  V [auth D],  W [auth D],  Y [auth E],  Z [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
3AT PDBBind:  1XFV Kd: 1.30e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.599α = 90
b = 319.285β = 90.22
c = 142.054γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



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