4J2P | pdb_00004j2p

Crystal structure of LuxF from Photobacterium leiognathi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.172 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Structural and biochemical properties of LuxF from Photobacterium leiognathi.

Bergner, T.Tabib, C.R.Winkler, A.Stipsits, S.Kayer, H.Lee, J.Malthouse, J.P.Mayhew, S.Muller, F.Gruber, K.Macheroux, P.

(2015) Biochim Biophys Acta 1854: 1466-1475

  • DOI: https://doi.org/10.1016/j.bbapap.2015.07.008
  • Primary Citation Related Structures: 
    4J2P

  • PubMed Abstract: 

    The lux-operon of bioluminescent bacteria contains the genes coding for the enzymes required for light emission. Some species of Photobacteria feature an additional gene, luxF, which shows similarity to luxA and luxB, the genes encoding the heterodimeric luciferase. Isolated dimeric LuxF binds four molecules of an unusually derivatized flavin, i.e., 6-(3'-(R)-myristyl)-FMN (myrFMN). In the present study we have heterologously expressed LuxF in Escherichia coli BL21 in order to advance our understanding of the protein's binding properties and its role in photobacterial bioluminescence. Structure determination by X-ray crystallography confirmed that apo-LuxF possesses four preorganized binding sites, which are further optimized by adjusting the orientation of amino acid side chains. To investigate the binding properties of recombinant LuxF we have isolated myrFMN from Photobacterium leiognathi S1. We found that LuxF binds myrFMN tightly with a dissociation constant of 80±20 nM demonstrating that the purified apo-form of LuxF is fully competent in myrFMN binding. In contrast to LuxF, binding of myrFMN to luciferase is much weaker (Kd=4.0±0.4 μM) enabling LuxF to prevent inhibition of the enzyme by scavenging myrFMN. Moreover, we have used apo-LuxF to demonstrate that myrFMN occurs in all Photobacteria tested, irrespective of the presence of luxF indicating that LuxF is not required for myrFMN biosynthesis.


  • Organizational Affiliation
    • Graz University of Technology, Institute of Biochemistry, Graz, Austria.

Macromolecule Content 

  • Total Structure Weight: 27.34 kDa 
  • Atom Count: 2,001 
  • Modeled Residue Count: 225 
  • Deposited Residue Count: 236 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Non-fluorescent flavoprotein236Photobacterium leiognathiMutation(s): 0 
Gene Names: luxF
UniProt
Find proteins for P09142 (Photobacterium leiognathi)
Explore P09142 
Go to UniProtKB:  P09142
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09142
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.172 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.18α = 90
b = 93.18β = 90
c = 115.43γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-05
    Type: Initial release
  • Version 1.1: 2017-12-13
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Refinement description