1NFP

STRUCTURAL REFINEMENT OF THE NON-FLUORESCENT FLAVOPROTEIN FROM PHOTOBACTERIUM LEIOGNATHI AT 1.60 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural refinement of the non-fluorescent flavoprotein from Photobacterium leiognathi at 1.60 A resolution.

Moore, S.A.James, M.N.

(1995) J.Mol.Biol. 249: 195-214

  • DOI: 10.1006/jmbi.1995.0289

  • PubMed Abstract: 
  • The crystallographically-determined structure of the non-fluorescent flavoprotein (NFP) from Photobacterium leiognathi, a homolog of the bacterial luciferase subunits, has been refined to a conventional R-factor [formula: see text] of 0.175 using syn ...

    The crystallographically-determined structure of the non-fluorescent flavoprotein (NFP) from Photobacterium leiognathi, a homolog of the bacterial luciferase subunits, has been refined to a conventional R-factor [formula: see text] of 0.175 using synchrotron data between 10.0 and 1.60 A resolution. The molecular structure is a homodimer of beta/alpha domains, the monomer having structural similarities to (beta alpha)8 barrel proteins. However, one beta-strand and three alpha-helices of a typical (beta alpha)8 domain are not present in the NFP structure. The refined structure of NFP consists of the 228 amino acid polypeptide, 191 water molecules, a sulfate ion, and two flavin mononucleotides (FMNs) each with a covalently-attached myristate (C14 fatty acid). Both flavin adducts are well-ordered and have exceptional electron density for both the FMN and the myristate moieties. Each flavin mononucleotide-myristate adduct is characterized by a stereospecific linkage (the S enantiomer) between C-6 of the flavin isoalloxazine ring and the C-3' atom of the fatty acyl chain. The stereospecific nature of this flavin-fatty acid linkage suggests that it is the result of an enzyme-catalyzed reaction, most likely the bioluminescence reaction itself. The myristate chains are buried from solvent in hydrophobic pockets in the interior of the protein. Four amino acid side-chains of the NFP polypeptide have been modeled with alternate conformations. Five of the protein's seven alpha-helices have classical C-capping boxes. NFP is dimeric and many of the extensive contacts at the dimer interface are mediated by hydrogen-bonded water molecules as well as by hydrophobic interactions. One of the myristate acyl chains sits between NFP monomers and contributes a significant portion of the hydrophobic interactions at the NFP dimer interface.


    Related Citations: 
    • Crystal Structure of a Flavoprotein Related to the Subunits of Bacterial Luciferase
      Moore, S.A.,James, M.N.G.,O'Kane, D.J.,Lee, J.
      (1993) Embo J. 12: 1767
    • Common Structural Features of the Luxf Protein and the Subunits of Bacterial Luciferase: Evidence for a (Beta(Slash)Alpha)8 Fold in Luciferase
      Moore, S.A.,James, M.N.G.
      (1994) Protein Sci. 3: 1914
    • Crystallization of Photobacterium Leiognathi Nfp, Non-Fluorescent Flavoprotein an Unusual Flavoprotein with Limited Sequence Identity to Bacterial Luciferase
      Moore, S.A.,James, M.N.G.,O'Kane, D.J.,Lee, J.
      (1992) J.Mol.Biol. 224: 523


    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LUXF GENE PRODUCT
A
228Photobacterium leiognathiMutation(s): 0 
Gene Names: luxF
Find proteins for P09142 (Photobacterium leiognathi)
Go to UniProtKB:  P09142
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
A
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 56.930α = 90.00
b = 92.230β = 90.00
c = 99.230γ = 90.00
Software Package:
Software NamePurpose
WEISdata reduction
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-06-03
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance