5LQ5

1.46 A resolution structure of PhnD1 from Prochlorococcus marinus (MIT 9301) in complex with phosphite


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.0 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: 10.1038/s41467-017-01226-8
  • Primary Citation of Related Structures:  5JVB, 5LQ1, 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 utili ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative phosphonate binding protein for ABC transporter
A
282Prochlorococcus marinus (strain MIT 9301)Gene Names: phnD1
Find proteins for A3PC74 (Prochlorococcus marinus (strain MIT 9301))
Go to UniProtKB:  A3PC74
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO3
Query on PO3

Download SDF File 
Download CCD File 
A
PHOSPHITE ION
O3 P
AQSJGOWTSHOLKH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.330α = 90.00
b = 57.610β = 107.15
c = 54.790γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUCCANEERmodel building
REFMACrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant 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 

  • Version 1.0: 2017-12-06
    Type: Initial release