6OTD

Globin sensor domain of AfGcHK in monomeric form, with imidazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    6OTD

  • PubMed Abstract: 
  • 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 ...

    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 WT 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 WT 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, Prague 2, 128 43 Czech Republic marketa.martinkova@natur.cuni.cz.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Globin-coupled histidine kinaseA161Anaeromyxobacter sp. Fw109-5Mutation(s): 0 
Gene Names: gchKAnae109_2438
EC: 2.7.13.3
UniProt
Find proteins for A7HD43 (Anaeromyxobacter sp. (strain Fw109-5))
Explore A7HD43 
Go to UniProtKB:  A7HD43
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
C [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
IMD (Subject of Investigation/LOI)
Query on IMD

Download Ideal Coordinates CCD File 
D [auth A], E [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 
  • Space Group: P 61 2 2
  • Diffraction Data DOI: 10.15785/SBGRID/715 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.44α = 90
b = 69.44β = 90
c = 113.364γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



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  (Full details and data files)

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