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

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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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: https://doi.org/10.1074/jbc.M117.817023
  • Primary Citation of Related Structures:  
    5OHE, 5OHF

  • PubMed Abstract: 

    The heme-based oxygen sensor histidine kinase Af GcHK is part of a two-component signal transduction system in bacteria. O 2 binding to the Fe(II) heme complex of its N-terminal globin domain strongly stimulates autophosphorylation at His 183 in its C-terminal kinase domain. The 6-coordinate heme Fe(III)-OH - and -CN - complexes of Af GcHK 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 Af GcHK 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 Af GcHK. We conclude that Af GcHK 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Globin-coupled histidine kinase
A, B, C, D, E
A, B, C, D, E, F, G, H
161Anaeromyxobacter sp. Fw109-5Mutation(s): 0 
Gene Names: gchKAnae109_2438
Find proteins for A7HD43 (Anaeromyxobacter sp. (strain Fw109-5))
Explore A7HD43 
Go to UniProtKB:  A7HD43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7HD43
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
N [auth C]
Q [auth D]
R [auth E]
I [auth A],
L [auth B],
N [auth C],
Q [auth D],
R [auth E],
V [auth F],
W [auth G],
Z [auth H]
C34 H32 Fe N4 O4
Query on CL

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K [auth B],
P [auth D],
T [auth E],
Y [auth G]
Query on CYN

Download Ideal Coordinates CCD File 
AA [auth H]
J [auth A]
M [auth B]
O [auth C]
S [auth E]
AA [auth H],
J [auth A],
M [auth B],
O [auth C],
S [auth E],
X [auth G]
Query on NA

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.069α = 90
b = 78.069β = 90
c = 441.819γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

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
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicLM2015043
Ministry of Education, Youth and Sports of the Czech RepublicCzech RepublicCZ.02.1.01/0.0/0.0/16_013/0001776

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2017-11-15
    Changes: Database references
  • Version 1.2: 2018-01-03
    Changes: Database references
  • Version 1.3: 2018-01-10
    Changes: Source and taxonomy
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description