1K90

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 396-402

  • DOI: 10.1038/415396a
  • Primary Citation of Related Structures:  
    1K8T, 1K93, 1K90

  • PubMed Abstract: 
  • Oedema factor, a calmodulin-activated adenylyl cyclase, is important in the pathogenesis of anthrax. Here we report the X-ray structures of oedema factor with and without bound calmodulin. Oedema factor shares no significant structural homology with ...

    Oedema factor, a calmodulin-activated adenylyl cyclase, is important in the pathogenesis of anthrax. Here we report the X-ray structures of oedema factor with and without bound calmodulin. Oedema factor shares no significant structural homology with mammalian adenylyl cyclases or other proteins. In the active site, 3'-deoxy-ATP and a single metal ion are well positioned for catalysis with histidine 351 as the catalytic base. This mechanism differs from the mechanism of two-metal-ion catalysis proposed for mammalian adenylyl cyclases. Four discrete regions of oedema factor form a surface that recognizes an extended conformation of calmodulin, which is very different from the collapsed conformation observed in other structures of calmodulin bound to effector peptides. On calmodulin binding, an oedema factor helical domain of relative molecular mass 15,000 undergoes a 15 A translation and a 30 degrees rotation away from the oedema factor catalytic core, which stabilizes a disordered loop and leads to enzyme activation. These allosteric changes provide the first molecular details of how calmodulin modulates one of its targets.


    Organizational Affiliation

    Ben-May Institute for Cancer Research, The University of Chicago, 924 East 57th Street, Chicago, Illinois 60637, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CALMODULIN-SENSITIVE ADENYLATE CYCLASEABC510Bacillus anthracisMutation(s): 0 
Gene Names: cyapXO1-122BXA0141GBAA_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
CALMODULINDEF148Homo sapiensMutation(s): 0 
Gene Names: CALM1CALMCAMCAM1
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
NIH Common Fund Data Resources
PHAROS  P0DP23
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3AT
Query on 3AT

Download CCD File 
A, B, C
3'-DEOXYADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
NLIHPCYXRYQPSD-BAJZRUMYSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.099α = 90
b = 166.1β = 90
c = 343.33γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Advisory, Derived calculations