5LJI

Streptococcus pneumonia TIGR4 flavodoxin: structural and biophysical characterization of a novel drug target


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Streptococcus pneumoniae TIGR4 Flavodoxin: Structural and Biophysical Characterization of a Novel Drug Target.

Rodriguez-Cardenas, A.Rojas, A.L.Conde-Gimenez, M.Velazquez-Campoy, A.Hurtado-Guerrero, R.Sancho, J.

(2016) Plos One 11: e0161020-e0161020

  • DOI: 10.1371/journal.pone.0161020
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Streptococcus pneumoniae (Sp) strain TIGR4 is a virulent, encapsulated serotype that causes bacteremia, otitis media, meningitis and pneumonia. Increased bacterial resistance and limited efficacy of the available vaccine to some serotypes complicate ...

    Streptococcus pneumoniae (Sp) strain TIGR4 is a virulent, encapsulated serotype that causes bacteremia, otitis media, meningitis and pneumonia. Increased bacterial resistance and limited efficacy of the available vaccine to some serotypes complicate the treatment of diseases associated to this microorganism. Flavodoxins are bacterial proteins involved in several important metabolic pathways. The Sp flavodoxin (Spfld) gene was recently reported to be essential for the establishment of meningitis in a rat model, which makes SpFld a potential drug target. To facilitate future pharmacological studies, we have cloned and expressed SpFld in E. coli and we have performed an extensive structural and biochemical characterization of both the apo form and its active complex with the FMN cofactor. SpFld is a short-chain flavodoxin containing 146 residues. Unlike the well-characterized long-chain apoflavodoxins, the Sp apoprotein displays a simple two-state thermal unfolding equilibrium and binds FMN with moderate affinity. The X-ray structures of the apo and holo forms of SpFld differ at the FMN binding site, where substantial rearrangement of residues at the 91-100 loop occurs to permit cofactor binding. This work will set up the basis for future studies aiming at discovering new potential drugs to treat S. pneumoniae diseases through the inhibition of SpFld.


    Organizational Affiliation

    Aragon Health Research Institute (IIS Aragón), University of Zaragoza, Zaragoza, Spain.,Fundación ARAID, Government of Aragón, Zaragoza, Spain.,Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Joint Unit IQFR-CSIC-BIFI, Joint Unit EEAD-CSIC-BIFI, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain.,Department of Biochemistry and Molecular and Cell Biology, University of Zaragoza, Zaragoza, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flavodoxin
A, C
148Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Mutation(s): 0 
Gene Names: flaV
Find proteins for Q8DPG4 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  Q8DPG4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

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

Download SDF File 
Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FMNKd: 83 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.187 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 101.676α = 90.00
b = 101.676β = 90.00
c = 68.285γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
MINECOSpainBFU2013-47064-P
MINECOSpainBFU2010-19504
MINECOSpainCTQ2013-44367-C2-2-P

Revision History 

  • Version 1.0: 2016-08-31
    Type: Initial release
  • Version 1.1: 2016-09-28
    Type: Database references