6QIM

Structure of AtPIP2;4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.328 
  • R-Value Observed: 0.331 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Characterization of aquaporin-driven hydrogen peroxide transport.

Wang, H.Schoebel, S.Schmitz, F.Dong, H.Hedfalk, K.

(2020) Biochim Biophys Acta Biomembr 1862: 183065-183065

  • DOI: https://doi.org/10.1016/j.bbamem.2019.183065
  • Primary Citation of Related Structures:  
    6QIM

  • PubMed Abstract: 

    Aquaporins are membrane-intrinsic proteins initially defined as water (H 2 O) channels in all organisms and subsequently found to have multiple substrate specificities, such as hydrogen peroxide (H 2 O 2 ). H 2 O 2 is a signaling molecule that partakes in immune responses where its transport is mediated by aquaporins. To shed further light on the molecular basis of the aquaporin function in H 2 O 2 transport, we have characterized an Arabidopsis thaliana aquaporin, AtPIP2;4, recombinantly produced to high yields in Pichia pastoris. Here, we present a newly established assay that allows detection of H 2 O 2 transport by purified aquaporins reconstituted into liposomes, enabling us to compare aquaporin homologues with respect to substrate specificity. To get additional insight into the structural determinants for aquaporin-mediated H 2 O 2 transport, we solved the 3D-structure of AtPIP2;4 to 3.7 Å resolution and found structural identity to the water channel from spinach (SoPIP2;1), with the difference that Cd 2+ cation is not required to retain the closed conformation. The transport specificities of the two plant aquaporins were compared to a human homologue, AQP1. Overall, we conclude that AtPIP2;4, SoPIP2;1 and hAQP1 are all transporters of both H 2 O and H 2 O 2 , but have different efficiencies for various specificities. Notably, all three homologues expedite H 2 O transport equally well while the plant aquaporins are more permeable to H 2 O 2 than hAQP1. Comparison of the structures indicates that the observed variations in H 2 O and H 2 O 2 transport cannot be explained by differences in the monomeric pore. Possibly, the determinants for transport specificities reside in the flexible domains outside the membrane core of these channels.


  • Organizational Affiliation

    Department of Plant Pathology, Nanjing Agricultural University, 1 Weigang, Nanjing 210095, China; Department of Chemistry and Molecular Biology, Gothenburg University, Box 462, 405 30 Göteborg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable aquaporin PIP2-4
A, B
259Arabidopsis thalianaMutation(s): 0 
Gene Names: PIP2-4At5g60660MUP24.9
Membrane Entity: Yes 
UniProt
Find proteins for Q9FF53 (Arabidopsis thaliana)
Explore Q9FF53 
Go to UniProtKB:  Q9FF53
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FF53
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.356 
  • R-Value Work: 0.328 
  • R-Value Observed: 0.331 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.985α = 90
b = 218.985β = 90
c = 100.637γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2020-01-15
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description