6RFM | pdb_00006rfm

Bordetella pertussis adenylate cyclase toxin transmembrane segment 411-490 in DPC micelles


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 50 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Negative charge of the AC-to-Hly linking segment modulates calcium-dependent membrane activities of Bordetella adenylate cyclase toxin.

Sukova, A.Bumba, L.Srb, P.Veverka, V.Stanek, O.Holubova, J.Chmelik, J.Fiser, R.Sebo, P.Masin, J.

(2020) Biochim Biophys Acta Biomembr 1862: 183310-183310

  • DOI: https://doi.org/10.1016/j.bbamem.2020.183310
  • Primary Citation Related Structures: 
    6RFM

  • PubMed Abstract: 

    Two distinct conformers of the adenylate cyclase toxin (CyaA) appear to accomplish its two parallel activities within target cell membrane. The translocating conformer would deliver the N-terminal adenylyl cyclase (AC) enzyme domain across plasma membrane into cytosol of cells, while the pore precursor conformer would assemble into oligomeric cation-selective pores and permeabilize cellular membrane. Both toxin activities then involve a membrane-interacting 'AC-to-Hly-linking segment' (residues 400 to 500). Here, we report the NMR structure of the corresponding CyaA 411 - 490 polypeptide in dodecylphosphocholine micelles and show that it consists of two α-helices linked by an unrestrained loop. The N-terminal α-helix (Gly418 to His439) remained solvent accessible, while the C-terminal α-helix (His457 to Phe485) was fully enclosed within detergent micelles. CyaA 411 - 490 weakly bound Ca 2+ ions (apparent K D 2.6 mM) and permeabilized negatively charged lipid vesicles. At high concentrations (10 μM) the CyaA 411 - 490 polypeptide formed stable conductance units in artificial lipid bilayers with applied voltage, suggesting its possible transmembrane orientation in the membrane-inserted toxin. Mutagenesis revealed that two clusters of negatively charged residues within the 'AC-to-Hly-linking segment' (Glu419 to Glu432 and Asp445 to Glu448) regulate the balance between the AC domain translocating and pore-forming capacities of CyaA in function of calcium concentration.


  • Organizational Affiliation
    • Institute of Microbiology of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 8.23 kDa 
  • Atom Count: 576 
  • Modeled Residue Count: 80 
  • Deposited Residue Count: 80 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bifunctional hemolysin/adenylate cyclase80Bordetella pertussisMutation(s): 0 
Gene Names: cyacyaABN118_0468
EC: 4.6.1.1
Membrane Entity: Yes 
UniProt
Find proteins for P0DKX7 (Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251))
Explore P0DKX7 
Go to UniProtKB:  P0DKX7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DKX7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 50 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2020-11-25
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Database references, Other
  • Version 1.3: 2024-06-19
    Changes: Data collection, Database references