4F1V

Subatomic resolution structure of a high affinity periplasmic phosphate-binding protein (PfluDING) bound with phosphate at pH 8.5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.88 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

The molecular basis of phosphate discrimination in arsenate-rich environments.

Elias, M.Wellner, A.Goldin-Azulay, K.Chabriere, E.Vorholt, J.A.Erb, T.J.Tawfik, D.S.

(2012) Nature 491: 134-137

  • DOI: 10.1038/nature11517
  • Primary Citation of Related Structures:  
    4F18, 4F19, 4F1U, 4F1V

  • PubMed Abstract: 
  • Arsenate and phosphate are abundant on Earth and have striking similarities: nearly identical pK(a) values, similarly charged oxygen atoms, and thermochemical radii that differ by only 4% (ref. 3). Phosphate is indispensable and arsenate is toxic, but this extensive similarity raises the question whether arsenate may substitute for phosphate in certain niches ...

    Arsenate and phosphate are abundant on Earth and have striking similarities: nearly identical pK(a) values, similarly charged oxygen atoms, and thermochemical radii that differ by only 4% (ref. 3). Phosphate is indispensable and arsenate is toxic, but this extensive similarity raises the question whether arsenate may substitute for phosphate in certain niches. However, whether it is used or excluded, discriminating phosphate from arsenate is a paramount challenge. Enzymes that utilize phosphate, for example, have the same binding mode and kinetic parameters as arsenate, and the latter's presence therefore decouples metabolism. Can proteins discriminate between these two anions, and how would they do so? In particular, cellular phosphate uptake systems face a challenge in arsenate-rich environments. Here we describe a molecular mechanism for this process. We examined the periplasmic phosphate-binding proteins (PBPs) of the ABC-type transport system that mediates phosphate uptake into bacterial cells, including two PBPs from the arsenate-rich Mono Lake Halomonas strain GFAJ-1. All PBPs tested are capable of discriminating phosphate over arsenate at least 500-fold. The exception is one of the PBPs of GFAJ-1 that shows roughly 4,500-fold discrimination and its gene is highly expressed under phosphate-limiting conditions. Sub-ångström-resolution structures of Pseudomonas fluorescens PBP with both arsenate and phosphate show a unique mode of binding that mediates discrimination. An extensive network of dipole-anion interactions, and of repulsive interactions, results in the 4% larger arsenate distorting a unique low-barrier hydrogen bond. These features enable the phosphate transport system to bind phosphate selectively over arsenate (at least 10(3) excess) even in highly arsenate-rich environments.


    Related Citations: 
    • Elucidation of the phosphate binding mode of DING proteins revealed by subangstrom X-ray crystallography.
      Liebschner, D., Elias, M., Moniot, S., Fournier, B., Scott, K., Jelsch, C., Guillot, B., Lecomte, C., Chabriere, E.
      (2009) J Am Chem Soc 131: 7879

    Organizational Affiliation

    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel. mikael.elias@weizmann.ac.il



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative alkaline phosphataseA381Pseudomonas fluorescens SBW25Mutation(s): 0 
Gene Names: PFLU_2427
UniProt
Find proteins for C3K8K1 (Pseudomonas fluorescens (strain SBW25))
Explore C3K8K1 
Go to UniProtKB:  C3K8K1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC3K8K1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PI
Query on PI

Download Ideal Coordinates CCD File 
B [auth A]HYDROGENPHOSPHATE ION
H O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.88 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.96α = 90
b = 124.9β = 116.31
c = 40.92γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2012-09-05
    Changes: Database references
  • Version 1.2: 2012-10-03
    Changes: Database references
  • Version 1.3: 2012-10-17
    Changes: Database references
  • Version 1.4: 2012-11-21
    Changes: Database references
  • Version 1.5: 2017-11-15
    Changes: Database references