4IIL

Crystal Structure of RfuA (TP0298) of T. pallidum Bound to Riboflavin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.122 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Evidence for an ABC-type riboflavin transporter system in pathogenic spirochetes.

Deka, R.K.Brautigam, C.A.Biddy, B.A.Liu, W.Z.Norgard, M.V.

(2013) mBio 4: e00615-e00612

  • DOI: 10.1128/mBio.00615-12
  • Primary Citation of Related Structures:  
    4IIL

  • PubMed Abstract: 
  • Bacterial transporter proteins are involved in the translocation of many essential nutrients and metabolites. However, many of these key bacterial transport systems remain to be identified, including those involved in the transport of riboflavin (vitamin B(2)) ...

    Bacterial transporter proteins are involved in the translocation of many essential nutrients and metabolites. However, many of these key bacterial transport systems remain to be identified, including those involved in the transport of riboflavin (vitamin B(2)). Pathogenic spirochetes lack riboflavin biosynthetic pathways, implying reliance on obtaining riboflavin from their hosts. Using structural and functional characterizations of possible ligand-binding components, we have identified an ABC-type riboflavin transport system within pathogenic spirochetes. The putative lipoprotein ligand-binding components of these systems from three different spirochetes were cloned, hyperexpressed in Escherichia coli, and purified to homogeneity. Solutions of all three of the purified recombinant proteins were bright yellow. UV-visible spectra demonstrated that these proteins were likely flavoproteins; electrospray ionization mass spectrometry and thin-layer chromatography confirmed that they contained riboflavin. A 1.3-Å crystal structure of the protein (TP0298) encoded by Treponema pallidum, the syphilis spirochete, demonstrated that the protein's fold is similar to the ligand-binding components of ABC-type transporters. The structure also revealed other salient details of the riboflavin binding site. Comparative bioinformatics analyses of spirochetal genomes, coupled with experimental validation, facilitated the discovery of this new ABC-type riboflavin transport system(s). We denote the ligand-binding component as riboflavin uptake transporter A (RfuA). Taken together, it appears that pathogenic spirochetes have evolved an ABC-type transport system (RfuABCD) for survival in their host environments, particularly that of the human host.


    Organizational Affiliation

    Department of Microbiology, University of Texas, Southwestern Medical Center, Dallas, Texas, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Membrane lipoprotein TpN38(b)A346Treponema pallidum subsp. pallidum str. NicholsMutation(s): 0 
Gene Names: tp0298tpn38TP_0298rfuA
Find proteins for Q56328 (Treponema pallidum (strain Nichols))
Explore Q56328 
Go to UniProtKB:  Q56328
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RBF
Query on RBF

Download Ideal Coordinates CCD File 
B [auth A]RIBOFLAVIN
C17 H20 N4 O6
AUNGANRZJHBGPY-SCRDCRAPSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
E [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.153 
  • R-Value Work: 0.121 
  • R-Value Observed: 0.122 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.955α = 90
b = 107.79β = 90
c = 72.881γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description