5LXQ

Structure of PRL-1 in complex with the Bateman domain of CNNM2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.335 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structural Basis of the Oncogenic Interaction of Phosphatase PRL-1 with the Magnesium Transporter CNNM2.

Gimenez-Mascarell, P.Oyenarte, I.Hardy, S.Breiderhoff, T.Stuiver, M.Kostantin, E.Diercks, T.Pey, A.L.Ereno-Orbea, J.Martinez-Chantar, M.L.Khalaf-Nazzal, R.Claverie-Martin, F.Muller, D.Tremblay, M.L.Martinez-Cruz, L.A.

(2017) J. Biol. Chem. 292: 786-801

  • DOI: 10.1074/jbc.M116.759944
  • Primary Citation of Related Structures:  
  • Also Cited By: 6G52

  • PubMed Abstract: 
  • Phosphatases of regenerating liver (PRLs), the most oncogenic of all protein-tyrosine phosphatases (PTPs), play a critical role in metastatic progression of cancers. Recent findings established a new paradigm by uncovering that their association with ...

    Phosphatases of regenerating liver (PRLs), the most oncogenic of all protein-tyrosine phosphatases (PTPs), play a critical role in metastatic progression of cancers. Recent findings established a new paradigm by uncovering that their association with magnesium transporters of the cyclin M (CNNM) family causes a rise in intracellular magnesium levels that promote oncogenic transformation. Recently, however, essential roles for regulation of the circadian rhythm and reproduction of the CNNM family have been highlighted. Here, we describe the crystal structure of PRL-1 in complex with the Bateman module of CNNM2 (CNNM2 BAT ), which consists of two cystathionine β-synthase (CBS) domains (IPR000664) and represents an intracellular regulatory module of the transporter. The structure reveals a heterotetrameric association, consisting of a disc-like homodimer of CNNM2 BAT bound to two independent PRL-1 molecules, each one located at opposite tips of the disc. The structure highlights the key role played by Asp-558 at the extended loop of the CBS2 motif of CNNM2 in maintaining the association between the two proteins and proves that the interaction between CNNM2 and PRL-1 occurs via the catalytic domain of the phosphatase. Our data shed new light on the structural basis underlying the interaction between PRL phosphatases and CNNM transporters and provides a hypothesis about the molecular mechanism by which PRL-1, upon binding to CNNM2, might increase the intracellular concentration of Mg 2+ thereby contributing to tumor progression and metastasis. The availability of this structure sets the basis for the rational design of compounds modulating PRL-1 and CNNM2 activities.


    Organizational Affiliation

    the Department of Physical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, 18071 Granada, Spain.,the Department of Pediatric Nephrology, Charité Universitäts Medizin, Berlin, 13353 Berlin, Germany, Dominik.Mueller@charite.de.,the Department of Biomedical Sciences, An-Najah National University, P. O. Box 7, Nablus, Palestinian Territory, and.,Division of Experimental Medicine, Department of Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada.,the Metabolomics Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain.,the Research Unit, Nuestra Señora de Candelaria University Hospital, 38010 Santa Cruz de Tenerife, Spain.,From the Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain, amartinez@cicbiogune.es.,Department of Biochemistry, and.,the Rosalind and Morris Goodman Cancer Research Centre.,the Department of Pediatric Nephrology, Charité Universitäts Medizin, Berlin, 13353 Berlin, Germany.,the Berlin Institute of Health, Berlin, Germany.,the Rosalind and Morris Goodman Cancer Research Centre, Michel.tremblay@mcgill.ca.,the In-Cell NMR Laboratory, Department of NMR-supported Structural Biology, Leibniz Institute of Molecular Pharmacology (FMP Berlin), Robert-Rössle Strasse 10, 13125 Berlin, Germany.,From the Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Technology Park of Bizkaia, 48160 Derio, Bizkaia, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein tyrosine phosphatase type IVA 1
B, C
196Mus musculusMutation(s): 0 
Gene Names: Ptp4a1 (Prl1)
EC: 3.1.3.48
Find proteins for Q63739 (Mus musculus)
Go to UniProtKB:  Q63739
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Metal transporter CNNM2
A, H
156Mus musculusMutation(s): 0 
Gene Names: Cnnm2 (Acdp2)
Find proteins for Q3TWN3 (Mus musculus)
Go to UniProtKB:  Q3TWN3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, H
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.335 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 166.930α = 90.00
b = 125.560β = 111.43
c = 61.040γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHENIXrefinement
Cootmodel building
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Database references
  • Version 1.2: 2016-12-21
    Type: Database references
  • Version 1.3: 2017-02-01
    Type: Database references
  • Version 1.4: 2019-06-12
    Type: Data collection, Structure summary