2Q9U

Crystal structure of the flavodiiron protein from Giardia intestinalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The O2-scavenging flavodiiron protein in the human parasite Giardia intestinalis

Di Matteo, A.Scandurra, F.M.Testa, F.Forte, E.Sarti, P.Brunori, M.Giuffre, A.

(2008) J.Biol.Chem. 283: 4061-4068

  • DOI: 10.1074/jbc.M705605200

  • PubMed Abstract: 
  • The flavodiiron proteins (FDP) are widespread among strict or facultative anaerobic prokaryotes, where they are involved in the response to nitrosative and/or oxidative stress. Unexpectedly, FDPs were fairly recently identified in a restricted group ...

    The flavodiiron proteins (FDP) are widespread among strict or facultative anaerobic prokaryotes, where they are involved in the response to nitrosative and/or oxidative stress. Unexpectedly, FDPs were fairly recently identified in a restricted group of microaerobic protozoa, including Giardia intestinalis, the causative agent of the human infectious disease giardiasis. The FDP from Giardia was expressed, purified, and extensively characterized by x-ray crystallography, stopped-flow spectroscopy, respirometry, and NO amperometry. Contrary to flavorubredoxin, the FDP from Escherichia coli, the enzyme from Giardia has high O(2)-reductase activity (>40 s(-1)), but very low NO-reductase activity (approximately 0.2 s(-1)); O(2) reacts with the reduced protein quite rapidly (milliseconds) and with high affinity (K(m) < or = 2 microM), producing H(2)O. The three-dimensional structure of the oxidized protein determined at 1.9A resolution shows remarkable similarities with prokaryotic FDPs. Consistent with HPLC analysis, the enzyme is a dimer of dimers with FMN and the non-heme di-iron site topologically close at the monomer-monomer interface. Unlike the FDP from Desulfovibrio gigas, the residue His-90 is a ligand of the di-iron site, in contrast with the proposal that ligation of this histidine is crucial for a preferential specificity for NO. We propose that in G. intestinalis the primary function of FDP is to efficiently scavenge O(2), allowing this microaerobic parasite to survive in the human small intestine, thus promoting its pathogenicity.


    Organizational Affiliation

    Department of Biochemical Sciences, CNR Institute of Molecular Biology and Pathology and Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza, University of Rome, Rome I-00185, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A-type flavoprotein
A, B
414Giardia intestinalisGene Names: fprA
Find proteins for Q86QZ1 (Giardia intestinalis)
Go to UniProtKB:  Q86QZ1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
NO3
Query on NO3

Download SDF File 
Download CCD File 
A, B
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
FEO
Query on FEO

Download SDF File 
Download CCD File 
A, B
MU-OXO-DIIRON
Fe2 O
NPMYUMBHPJGBFA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 111.967α = 90.00
b = 115.059β = 90.00
c = 67.732γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
ADSCdata collection
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance