6B67

Human PP2Calpha (PPM1A) complexed with cyclic peptide c(MpSIpYVA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A trapped human PPM1A-phosphopeptide complex reveals structural features critical for regulation of PPM protein phosphatase activity.

Debnath, S.Kosek, D.Tagad, H.D.Durell, S.R.Appella, D.H.Acevedo, R.Grishaev, A.Dyda, F.Appella, E.Mazur, S.J.

(2018) J. Biol. Chem. 293: 7993-8008

  • DOI: 10.1074/jbc.RA117.001213

  • PubMed Abstract: 
  • Metal-dependent protein phosphatases (PPM) are evolutionarily unrelated to other serine/threonine protein phosphatases and are characterized by their requirement for supplementation with millimolar concentrations of Mg <sup>2+ </sup> or Mn <sup>2+ </ ...

    Metal-dependent protein phosphatases (PPM) are evolutionarily unrelated to other serine/threonine protein phosphatases and are characterized by their requirement for supplementation with millimolar concentrations of Mg 2+ or Mn 2+ ions for activity in vitro The crystal structure of human PPM1A (also known as PP2Cα), the first PPM structure determined, displays two tightly bound Mn 2+ ions in the active site and a small subdomain, termed the Flap, located adjacent to the active site. Some recent crystal structures of bacterial or plant PPM phosphatases have disclosed two tightly bound metal ions and an additional third metal ion in the active site. Here, the crystal structure of the catalytic domain of human PPM1A, PPM1A cat , complexed with a cyclic phosphopeptide, c(MpSIpYVA), a cyclized variant of the activation loop of p38 MAPK (a physiological substrate of PPM1A), revealed three metal ions in the active site. The PPM1A cat D146E-c(MpSIpYVA) complex confirmed the presence of the anticipated third metal ion in the active site of metazoan PPM phosphatases. Biophysical and computational methods suggested that complex formation results in a slightly more compact solution conformation through reduced conformational flexibility of the Flap subdomain. We also observed that the position of the substrate in the active site allows solvent access to the labile third metal-binding site. Enzyme kinetics of PPM1A cat toward a phosphopeptide substrate supported a random-order, bi-substrate mechanism, with substantial interaction between the bound substrate and the labile metal ion. This work illuminates the structural and thermodynamic basis of an innate mechanism regulating the activity of PPM phosphatases.


    Organizational Affiliation

    Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, Maryland 20892.,the Laboratories of Molecular Biology and.,From the Laboratory of Cell Biology, Center for Cancer Research, NCI, and.,the National Institute of Standards and Technology, Gaithersburg, Maryland 20899.,the Institute for Bioscience and Biotechnology Research, Rockville, Maryland 20850, and.,From the Laboratory of Cell Biology, Center for Cancer Research, NCI, and mazurs@mail.nih.gov.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein phosphatase 1A
A, B, C
296Homo sapiensMutation(s): 1 
Gene Names: PPM1A (PPPM1A)
EC: 3.1.3.16
Find proteins for P35813 (Homo sapiens)
Go to Gene View: PPM1A
Go to UniProtKB:  P35813
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
cyclic peptide c(MpSIpYVA)
D, E, F
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
48V
Query on 48V
D, E, F
peptide-likeC5 H10 N2 O3 S

--

SEP
Query on SEP
D, E, F
L-PEPTIDE LINKINGC3 H8 N O6 PSER
PTR
Query on PTR
D, E, F
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.169 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 159.030α = 90.00
b = 89.570β = 113.86
c = 70.050γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-10-01 
  • Released Date: 2018-04-11 
  • Deposition Author(s): Dyda, F., Kosek, D.

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-06-06
    Type: Data collection, Database references