6NUU

Structure of Calcineurin mutant in complex with NHE1 peptide

  • Classification: HYDROLASE/Calcium Binding Protein
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2019-02-02 Released: 2019-07-03 
  • Deposition Author(s): Wang, X., Page, R., Peti, W.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular basis for the binding and selective dephosphorylation of Na+/H+exchanger 1 by calcineurin.

Hendus-Altenburger, R.Wang, X.Sjogaard-Frich, L.M.Pedraz-Cuesta, E.Sheftic, S.R.Bendsoe, A.H.Page, R.Kragelund, B.B.Pedersen, S.F.Peti, W.

(2019) Nat Commun 10: 3489-3489

  • DOI: 10.1038/s41467-019-11391-7
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Very little is known about how Ser/Thr protein phosphatases specifically recruit and dephosphorylate substrates. Here, we identify how the Na + /H + -exchanger 1 (NHE1), a key regulator of cellular pH homeostasis, is regulated b ...

    Very little is known about how Ser/Thr protein phosphatases specifically recruit and dephosphorylate substrates. Here, we identify how the Na + /H + -exchanger 1 (NHE1), a key regulator of cellular pH homeostasis, is regulated by the Ser/Thr phosphatase calcineurin (CN). NHE1 activity is increased by phosphorylation of NHE1 residue T779, which is specifically dephosphorylated by CN. While it is known that Ser/Thr protein phosphatases prefer pThr over pSer, we show that this preference is not key to this exquisite CN selectivity. Rather a combination of molecular mechanisms, including recognition motifs, dynamic charge-charge interactions and a substrate interaction pocket lead to selective dephosphorylation of pT779. Our data identify T779 as a site regulating NHE1-mediated cellular acid extrusion and provides a molecular understanding of NHE1 substrate selection by CN, specifically, and how phosphatases recruit specific substrates, generally.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Arizona, 1041 E. Lowell St., Tucson, AZ, 85721, USA. wolfgangpeti@email.arizona.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoformA372Homo sapiensMutation(s): 2 
Gene Names: PPP3CACALNACNA
EC: 3.1.3.16
Find proteins for Q08209 (Homo sapiens)
Explore Q08209 
Go to UniProtKB:  Q08209
NIH Common Fund Data Resources
PHAROS  Q08209
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calcineurin subunit B type 1B156Homo sapiensMutation(s): 0 
Gene Names: PPP3R1CNA2CNB
Find proteins for P63098 (Homo sapiens)
Explore P63098 
Go to UniProtKB:  P63098
NIH Common Fund Data Resources
PHAROS  P63098
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Sodium/hydrogen exchanger 1C48Homo sapiensMutation(s): 0 
Gene Names: SLC9A1APNH1NHE1
Find proteins for P19634 (Homo sapiens)
Explore P19634 
Go to UniProtKB:  P19634
NIH Common Fund Data Resources
PHAROS  P19634
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.303α = 90
b = 125.966β = 90
c = 127.352γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SAINTdata reduction
SADABSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS091336
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM098482

Revision History 

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence