6OTD

Globin sensor domain of AfGcHK in monomeric form, with imidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Disruption of the dimerization interface of the sensing domain in the dimeric heme-based oxygen sensorAfGcHK abolishes bacterial signal transduction.

Skalova, T.Lengalova, A.Dohnalek, J.Harlos, K.Mihalcin, P.Kolenko, P.Stranava, M.Blaha, J.Shimizu, T.Martinkova, M.

(2020) J.Biol.Chem. 295: 1587-1597

  • DOI: 10.1074/jbc.RA119.011574

  • PubMed Abstract: 
  • The heme-based oxygen sensor protein <i>Af </i>GcHK is a globin-coupled histidine kinase in the soil bacterium <i>Anaeromyxobacter </i> sp. Fw109-5. Its C-terminal functional domain exhibits autophosphorylation activity induced by oxygen binding to ...

    The heme-based oxygen sensor protein Af GcHK is a globin-coupled histidine kinase in the soil bacterium Anaeromyxobacter sp. Fw109-5. Its C-terminal functional domain exhibits autophosphorylation activity induced by oxygen binding to the heme Fe(II) complex located in the oxygen-sensing N-terminal globin domain. A detailed understanding of the signal transduction mechanisms in heme-containing sensor proteins remains elusive. Here, we investigated the role of the globin domain's dimerization interface in signal transduction in Af GcHK. We present a crystal structure of a monomeric imidazole-bound Af GcHK globin domain at 1.8 Å resolution, revealing that the helices of the wild-type globin dimer are under tension and suggesting that Tyr-15 plays a role in both this tension and the globin domain's dimerization. Biophysical experiments revealed that whereas the isolated wild-type globin domain is dimeric in solution, the Y15A and Y15G variants in which Tyr-15 is replaced with Ala or Gly, respectively, are monomeric. Additionally, we found that although the dimerization of the full-length protein is preserved via the kinase domain dimerization interface in all variants, full-length Af GcHK variants bearing the Y15A or Y15G substitutions lack enzymatic activity. The combined structural and biophysical results presented here indicate that Tyr-15 plays a key role in the dimerization of the globin domain of Af GcHK and that globin domain dimerization is essential for internal signal transduction and autophosphorylation in this protein. These findings provide critical insights into the signal transduction mechanism of the histidine kinase  Af GcHK from Anaeromyxobacter .


    Organizational Affiliation

    Department of Biochemistry, Faculty of Science, Charles University, Czech Republic.,Department of Biochemistry, Department of Biochemistry, Faculty of Science, Charles University, Czech Republic.,FNSPE, Czech Technical University in Prague, Czech Republic.,University of Oxford.,Institute of Biotechnology CAS, v.v.i., Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University.,Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Globin-coupled histidine kinase
A
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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
IMD
Query on IMD

Download SDF File 
Download CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 69.440α = 90.00
b = 69.440β = 90.00
c = 113.364γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Czech Republic)Czech RepublicLM2015043
European Regional Development FundCzech RepublicCZ.02.1.01/0.0/0.0/16_013/0001776

Revision History 

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2020-01-22
    Type: Database references
  • Version 1.2: 2020-02-19
    Type: Database references