5TSR

Crystal structure of PRL-3 phosphatase in complex with the Bateman domain of CNNM3 magnesium transporter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

PRL3 phosphatase active site is required for binding the putative magnesium transporter CNNM3.

Zhang, H.Kozlov, G.Li, X.Wu, H.Gulerez, I.Gehring, K.

(2017) Sci Rep 7: 48-48

  • DOI: https://doi.org/10.1038/s41598-017-00147-2
  • Primary Citation of Related Structures:  
    5K23, 5K24, 5K25, 5TSR

  • PubMed Abstract: 

    The phosphatases of regenerating liver (PRLs) are involved in tumorigenesis and metastatic cancer yet their cellular function remains unclear. Recent reports have shown PRL phosphatases bind tightly to the CNNM family of membrane proteins to regulate magnesium efflux. Here, we characterize the interactions between the CBS-pair (Bateman) domain of CNNM3 and either PRL2 or PRL3 using X-ray crystallography, isothermal titration calorimetry, and activity assays. We report four new crystal structures of PRL proteins bound to the CNNM3 CBS-pair domain that reveal the effects of cysteine disulphide formation and nucleotide binding on complex formation. We use comprehensive mutagenesis of the PRL3 catalytic site to quantify the importance of different PRL amino acids, including cysteine 104, leucine 108, and arginine 110, for CNNM binding and phosphatase activity. We show the PRL3 R138E mutant is selectively deficient in CNNM3 binding with the potential to distinguish between the downstream effects of phosphatase and CNNM-binding activities in vivo. Through a novel activity assay, we show that PRL3 has magnesium-sensitive phosphatase activity with ATP and other nucleotides. Our results identify a strong correlation between phosphatase activity and CNNM binding and support the contention that PRL function as pseudophosphatases regulated by chemical modifications of their catalytic cysteine.


  • Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, Quebec, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein tyrosine phosphatase type IVA 3
A, C
172Homo sapiensMutation(s): 1 
Gene Names: PTP4A3PRL3
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for O75365 (Homo sapiens)
Explore O75365 
Go to UniProtKB:  O75365
PHAROS:  O75365
GTEx:  ENSG00000184489 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75365
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Metal transporter CNNM3
B, D
155Homo sapiensMutation(s): 0 
Gene Names: CNNM3ACDP3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NE01 (Homo sapiens)
Explore Q8NE01 
Go to UniProtKB:  Q8NE01
PHAROS:  Q8NE01
GTEx:  ENSG00000168763 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NE01
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.241 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.339α = 90
b = 125.146β = 102.21
c = 52.042γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description