5LQ1

1.41 A resolution structure of PtxB from Trichodesmium erythraeum IMS101 in complex with methylphosphonate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The molecular basis of phosphite and hypophosphite recognition by ABC-transporters.

Bisson, C.Adams, N.B.P.Stevenson, B.Brindley, A.A.Polyviou, D.Bibby, T.S.Baker, P.J.Hunter, C.N.Hitchcock, A.

(2017) Nat Commun 8: 1746-1746

  • DOI: https://doi.org/10.1038/s41467-017-01226-8
  • Primary Citation of Related Structures:  
    5JVB, 5LQ1, 5LQ5, 5LQ8, 5LV1, 5ME4, 5O2J, 5O2K, 5O37

  • PubMed Abstract: 

    Inorganic phosphate is the major bioavailable form of the essential nutrient phosphorus. However, the concentration of phosphate in most natural habitats is low enough to limit microbial growth. Under phosphate-depleted conditions some bacteria utilise phosphite and hypophosphite as alternative sources of phosphorus, but the molecular basis of reduced phosphorus acquisition from the environment is not fully understood. Here, we present crystal structures and ligand binding affinities of periplasmic binding proteins from bacterial phosphite and hypophosphite ATP-binding cassette transporters. We reveal that phosphite and hypophosphite specificity results from a combination of steric selection and the presence of a P-H…π interaction between the ligand and a conserved aromatic residue in the ligand-binding pocket. The characterisation of high affinity and specific transporters has implications for the marine phosphorus redox cycle, and might aid the use of phosphite as an alternative phosphorus source in biotechnological, industrial and agricultural applications.


  • Organizational Affiliation

    Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphonate ABC transporter, periplasmic phosphonate-binding protein
A, B
280Trichodesmium erythraeum IMS101Mutation(s): 0 
Gene Names: Tery_0366
UniProt
Find proteins for Q119I9 (Trichodesmium erythraeum (strain IMS101))
Explore Q119I9 
Go to UniProtKB:  Q119I9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ119I9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GB
Query on GB

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
METHYLPHOSPHONIC ACID ESTER GROUP
C H5 O3 P
YACKEPLHDIMKIO-UHFFFAOYSA-N
EDO
Query on EDO

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

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
G [auth B],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.481α = 84.82
b = 53.703β = 78.26
c = 66.388γ = 69.74
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M000265/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M011305/1
European Research CouncilUnited Kingdom338895
NERC/A. G. Leventis Foundation PhD studentshipUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description