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 
  • R-Value Observed: 0.165 

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 U S A 106: 21854-21859

  • DOI: 10.1073/pnas.0904793106
  • Primary Citation of Related Structures:  
    3GFV

  • 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 transporters for iron scavenging using xenosiderophores ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized ABC transporter solute-binding protein yclQA, B303Bacillus subtilis subsp. subtilis str. 168Mutation(s): 0 
Gene Names: BSU03830yclQ
UniProt
Find proteins for P94421 (Bacillus subtilis (strain 168))
Explore P94421 
Go to UniProtKB:  P94421
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ASN
Query on ASN

Download Ideal Coordinates CCD File 
D [auth B]ASPARAGINE
C4 H8 N2 O3
DCXYFEDJOCDNAF-REOHCLBHSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, BL-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 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.602α = 90
b = 35.15β = 91.53
c = 95.433γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXCDphasing
SHELXDphasing
MLPHAREphasing
DMmodel building
SOLVEphasing
RESOLVEmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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