1XJ3

bjFixLH in unliganded ferrous form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of Deoxy and CO-Bound bjFixLH Reveal Details of Ligand Recognition and Signaling

Key, J.Moffat, K.

(2005) Biochemistry 44: 4627-4635

  • DOI: 10.1021/bi047942r
  • Primary Citation of Related Structures:  1XJ2, 1XJ4, 1XJ6

  • PubMed Abstract: 
  • Rhizobia directly regulate the expression of genes required for symbiotic nitrogen fixation in response to oxygen concentration via the sensor protein FixL. The N-terminal PAS domain of FixL contains a histidine-coordinated heme and regulates the act ...

    Rhizobia directly regulate the expression of genes required for symbiotic nitrogen fixation in response to oxygen concentration via the sensor protein FixL. The N-terminal PAS domain of FixL contains a histidine-coordinated heme and regulates the activity of its effector domain, a C-terminal histidine kinase, in response to binding of oxygen and other ligands at the heme. To further investigate ligand-induced inhibition of FixL, we have determined the crystal structures of the heme domain in both the deoxy state and bound to carbon monoxide, a weak inhibitor of FixL kinase activity. Structures collected at room temperature are presented in each state from two crystallographic space groups at 1.8 and 2 A resolution. These structures reveal displacement of the residues of the H(beta) and I(beta) strands by Leu236 upon CO binding, and this structural change propagates more than 15 A to a region of the structure implicated in signal transduction in PAS proteins. Displacement of residues Ile215, Ile216, and Gly217 in the FG loop is also evident, accompanied by the movement of heme propionate 6 upon change in iron ligation. CO binding increases the temperature factors in the FG loop of the protein and disorders the side chain of Arg206, a conserved residue involved in the FG loop switch mechanism. We relate these results to structural changes in other PAS sensor domains and their involvement in catalytic control.


    Organizational Affiliation

    Department of Biochemistry, University of Chicago, Chicago, Illinois 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sensor protein fixL
A
116Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)Gene Names: fixL
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 SDF File 
Download CCD File 
A
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: 1.9 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.214 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 128.644α = 90.00
b = 128.644β = 90.00
c = 58.695γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
EPMRphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2004-09-22 
  • Released Date: 2005-03-29 
  • Deposition Author(s): Key, J., Moffat, K.

Revision History 

  • Version 1.0: 2005-03-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance