5K25

Crystal structure of human phosphatase PRL-2 in complex with the ADP-bound Bateman domain of human magnesium transporter CNNM3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/s41598-017-00147-2
  • Primary Citation of Related Structures:  

  • 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 ...

    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. kalle.gehring@mcgill.ca.,School of Chemical Engineering, Northwest University, Xi'an, 710069, China.,Department of Biochemistry, McGill University, Montreal, Quebec, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein tyrosine phosphatase type IVA 2
A
190Homo sapiensMutation(s): 0 
Gene Names: PTP4A2 (PRL2, PTPCAAX2)
EC: 3.1.3.48
Find proteins for Q12974 (Homo sapiens)
Go to Gene View: PTP4A2
Go to UniProtKB:  Q12974
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Metal transporter CNNM3
C
156Homo sapiensMutation(s): 0 
Gene Names: CNNM3 (ACDP3)
Find proteins for Q8NE01 (Homo sapiens)
Go to Gene View: CNNM3
Go to UniProtKB:  Q8NE01
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
C
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.232 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 52.152α = 90.00
b = 124.401β = 90.00
c = 164.305γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2018-10-03
    Type: Data collection, Database references, Derived calculations