5OHF

Globin sensor domain of AfGcHK (FeIII form) in complex with cyanide, partially reduced


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction.

Stranava, M.Man, P.Skalova, T.Kolenko, P.Blaha, J.Fojtikova, V.Martinek, V.Dohnalek, J.Lengalova, A.Rosulek, M.Shimizu, T.Martinkova, M.

(2017) J. Biol. Chem. 292: 20921-20935

  • DOI: 10.1074/jbc.M117.817023
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The heme-based oxygen sensor histidine kinase AfGcHK is part of a two-component signal transduction system in bacteria. O2 binding to the Fe(II) heme complex of its N-terminal globin domain strongly stimulates autophosphorylation at His183 in its C-t ...

    The heme-based oxygen sensor histidine kinase AfGcHK is part of a two-component signal transduction system in bacteria. O2 binding to the Fe(II) heme complex of its N-terminal globin domain strongly stimulates autophosphorylation at His183 in its C-terminal kinase domain. The 6-coordinate heme Fe(III)-OH- and -CN- complexes of AfGcHK are also active, but the 5-coordinate heme Fe(II) complex and the heme-free apo-form are inactive. Here, we determined the crystal structures of the isolated dimeric globin domains of the active Fe(III)-CN- and inactive 5-coordinate Fe(II) forms, revealing striking structural differences on the heme-proximal side of the globin domain. Using hydrogen/deuterium exchange coupled with mass spectrometry to characterize the conformations of the active and inactive forms of full-length AfGcHK in solution, we investigated the intramolecular signal transduction mechanisms. Major differences between the active and inactive forms were observed on the heme-proximal side (helix H5), at the dimerization interface (helices H6 and H7 and loop L7) of the globin domain and in the ATP-binding site (helices H9 and H11) of the kinase domain. Moreover, separation of the sensor and kinase domains, which deactivates catalysis, increased the solvent exposure of the globin domain-dimerization interface (helix H6) as well as the flexibility and solvent exposure of helix H11. Together, these results suggest that structural changes at the heme-proximal side, the globin domain-dimerization interface, and the ATP-binding site are important in the signal transduction mechanism of AfGcHK. We conclude that AfGcHK functions as an ensemble of molecules sampling at least two conformational states.


    Organizational Affiliation

    From the Department of Biochemistry, Faculty of Science, Charles University, Hlavova (Albertov) 2030/8, Prague 2, 128 43 Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Globin-coupled histidine kinase
A, B, C, D, E, F, G, H
161Anaeromyxobacter sp. (strain Fw109-5)Mutation(s): 0 
Gene Names: gchK
EC: 2.7.13.3
Find proteins for A7HD43 (Anaeromyxobacter sp. (strain Fw109-5))
Go to UniProtKB:  A7HD43
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CYN
Query on CYN

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, C, D, E, G
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.190 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 77.685α = 90.00
b = 77.685β = 90.00
c = 441.238γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic15-19883S
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicCZ.1.05/1.1.00/02.109
Grant Agency of the Czech Technical UniversityCzech RepublicSGS16/246/OHK4/3T/14

Revision History 

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Database references
  • Version 1.2: 2018-01-03
    Type: Database references