7OBE

X-ray structure of the phosphatase PAPP5 from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conformational Change of Tetratricopeptide Repeats Region Triggers Activation of Phytochrome-Associated Protein Phosphatase 5.

von Horsten, S.Essen, L.O.

(2021) Front Plant Sci 12: 733069-733069

  • DOI: https://doi.org/10.3389/fpls.2021.733069
  • Primary Citation of Related Structures:  
    7OBE

  • PubMed Abstract: 

    Phytochrome activity is not only controlled by light but also by post-translational modifications, e. g. phosphorylation. One of the phosphatases responsible for plant phytochrome dephosphorylation and thereby increased activity is the phytochrome-associated protein phosphatase 5 (PAPP5). We show that PAPP5 recognizes phospho-site mimicking mutants of phytochrome B, when being activated by arachidonic acid (AA). Addition of AA to PAPP5 decreases the α-helical content as tracked by CD-spectroscopy. These changes correspond to conformational changes of the regulatory tetratricopeptide repeats (TPR) region as shown by mapping data from hydrogen deuterium exchange mass spectrometry onto a 3.0 Å crystal structure of PAPP5. Surprisingly, parts of the linker between the TPR and PP2A domains and of the so-called C-terminal inhibitory motif exhibit reduced deuterium uptake upon AA-binding. Molecular dynamics analyses of PAPP5 complexed to a phyB phosphopeptide show that this C-terminal motif remains associated with the TPR region in the substrate bound state, suggesting that this motif merely serves for restricting the orientations of the TPR region relative to the catalytic PP2A domain. Given the high similarity to mammalian PP5 these data from a plant ortholog show that the activation mode of these PPP-type protein phosphatases is highly conserved.


  • Organizational Affiliation

    Department of Biochemistry, Faculty of Chemistry, Philipps-University, Marburg, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Serine/threonine-protein phosphatase 5
A, B
504Arabidopsis thalianaMutation(s): 0 
Gene Names: PAPP5PP5At2g42810F7D19.19
EC: 3.1.3.16
UniProt
Find proteins for Q84XU2 (Arabidopsis thaliana)
Explore Q84XU2 
Go to UniProtKB:  Q84XU2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84XU2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.58α = 90
b = 103.01β = 95.564
c = 95.06γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyES152/10

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description