2CMN

A Proximal Arginine Residue in the Switching Mechanism of the FixL Oxygen Sensor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Proximal Arginine R206 Participates in Switching of the Bradyrhizobium Japonicum Fixl Oxygen Sensor

Gilles-Gonzalez, M.-A.Caceres, A.I.Silva Sousa, E.H.Tomchick, D.R.Brautigam, C.A.Gonzalez, C.Machius, M.

(2006) J Mol Biol 360: 80

  • DOI: 10.1016/j.jmb.2006.04.054
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • In oxygen-sensing PAS domains, a conserved polar residue on the proximal side of the heme cofactor, usually arginine or histidine, interacts alternately with the protein in the "on-state" or the heme edge in the "off-state" but does not contact the b ...

    In oxygen-sensing PAS domains, a conserved polar residue on the proximal side of the heme cofactor, usually arginine or histidine, interacts alternately with the protein in the "on-state" or the heme edge in the "off-state" but does not contact the bound ligand directly. We assessed the contributions of this residue in Bradyrhizobium japonicum FixL by determining the effects of an R206A substitution on the heme-PAS structure, ligand affinity, and regulatory capacity. The crystal structures of the unliganded forms of the R206A and wild-type BjFixL heme-PAS domains were similar, except for a more ruffled porphyrin ring in R206A BjFixL and a relaxation of the H214 residue and heme propionate 7 due to their lost interactions. The oxygen affinity of R206A BjFixL (Kd approximately 350 microM) was 2.5 times lower than that of BjFixL, and this was due to a higher off-rate constant for the R206A variant. The enzymatic activities of the unliganded "on-state" forms, either deoxy or met-R206A BjFixL, were comparable to each other and slightly lower (twofold less) than those of the corresponding BjFixL species. The most striking difference between the two proteins was in the enzymatic activities of the liganded "off-state" forms. In particular, saturation with a regulatory ligand (the Fe(III) form with cyanide) caused a >2000-fold inhibition of the BjFixL phosphorylation of BjFixJ, but a 140-fold inhibition of this catalytic activity in R206A BjFixL. Thus, in oxygen-sensing PAS domains, the interactions of polar residues with the heme edge couple the heme-binding domain to a transmitter during signal transduction.


    Related Citations: 
    • The Regulatory Status of the Fixl- and Fixj-Like Genes in Bradyrhizobium Japonicum May be Different from that in Rhizobium Meliloti
      Anthamatten, D., Hennecke, H.
      (1991) Mol Gen Genet 225: 38
    • A Distal Arginine in Oxygen-Sensing Heme-Pas Domains is Essential to Ligand Binding, Signal Transduction, and Structure.
      Dunham, C.M., Dioum, E.M., Tuckerman, J.R., Gonzalez, G., Scott, W.G., Gilles-Gonzalez, M.A.
      (2003) Biochemistry 42: 7701

    Organizational Affiliation

    Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA. magg@bochem.swmed.edu



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SENSOR PROTEIN FIXL
A
130Bradyrhizobium japonicumMutation(s): 1 
EC: 2.7.13.3
Find proteins for P23222 (Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110))
Go to UniProtKB:  P23222
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.117α = 90
b = 127.117β = 90
c = 58.569γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-04-03
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-15
    Changes: Data collection, Experimental preparation