3GFV

Crystal Structure of Petrobactin-binding Protein YclQ from Bacillu subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of a Bacillus subtilis transporter for petrobactin, an anthrax stealth siderophore.

Zawadzka, A.M.Kim, Y.Maltseva, N.Nichiporuk, R.Fan, Y.Joachimiak, A.Raymond, K.N.

(2009) Proc.Natl.Acad.Sci.USA 106: 21854-21859

  • DOI: 10.1073/pnas.0904793106

  • PubMed Abstract: 
  • Iron deprivation activates the expression of components of the siderophore-mediated iron acquisition systems in Bacillus subtilis, including not only the synthesis and uptake of its siderophore bacillibactin but also expression of multiple ABC transp ...

    Iron deprivation activates the expression of components of the siderophore-mediated iron acquisition systems in Bacillus subtilis, including not only the synthesis and uptake of its siderophore bacillibactin but also expression of multiple ABC transporters for iron scavenging using xenosiderophores. The yclNOPQ operon is shown to encode the complete transporter for petrobactin (PB), a photoreactive 3,4-catecholate siderophore produced by many members of the B. cereus group, including B. anthracis. Isogenic disruption mutants in the yclNOPQ transporter, including permease YclN, ATPase YclP, and a substrate-binding protein YclQ, are unable to use either PB or the photoproduct of FePB (FePB(nu)) for iron delivery and growth, in contrast to the wild-type B. subtilis. Complementation of the mutations with the copies of the respective genes restores this capability. The YclQ receptor binds selectively iron-free and ferric PB, the PB precursor, 3,4-dihydroxybenzoic acid (3,4-DHB), and FePB(nu) with high affinity; the ferric complexes are seen in ESI-MS, implying strong electrostatic interaction between the protein-binding pocket and siderophore. The first structure of a gram-positive siderophore receptor is presented. The 1.75-A crystal structure of YclQ reveals a bilobal periplasmic binding protein (PBP) fold consisting of two alpha/beta/alpha sandwich domains connected by a long alpha-helix with the binding pocket containing conserved positively charged and aromatic residues and large enough to accommodate FePB. Orthologs of the B. subtilis PB-transporter YclNOPQ in PB-producing Bacilli are likely contributors to the pathogenicity of these species and provide a potential target for antibacterial strategies.


    Organizational Affiliation

    Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Uncharacterized ABC transporter solute-binding protein yclQ
A, B
303Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: yclQ
Find proteins for P94421 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P94421
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ASN
Query on ASN

Download SDF File 
Download CCD File 
B
ASPARAGINE
C4 H8 N2 O3
DCXYFEDJOCDNAF-REOHCLBHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 82.602α = 90.00
b = 35.150β = 91.53
c = 95.433γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data collection
DMmodel building
SOLVEphasing
RESOLVEmodel building
DMphasing
MLPHAREphasing
HKL-3000phasing
SHELXDphasing
HKL-3000data scaling
SHELXCDphasing
SBC-Collectdata collection
PHENIXrefinement
RESOLVEphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description