4RAG

CRYSTAL STRUCTURE of PPC2A-D38K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The catalytic role of the M2 metal ion in PP2C alpha

Pan, C.Tang, J.Y.Xu, Y.F.Xiao, P.Liu, H.D.Wang, H.A.Wang, W.B.Meng, F.G.Yu, X.Sun, J.P.

(2015) Sci Rep 5: 8560-8560

  • DOI: 10.1038/srep08560
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PP2C family phosphatases (the type 2C family of protein phosphatases; or metal-dependent phosphatase, PPM) constitute an important class of signaling enzymes that regulate many fundamental life activities. All PP2C family members have a conserved bin ...

    PP2C family phosphatases (the type 2C family of protein phosphatases; or metal-dependent phosphatase, PPM) constitute an important class of signaling enzymes that regulate many fundamental life activities. All PP2C family members have a conserved binuclear metal ion active center that is essential for their catalysis. However, the catalytic role of each metal ion during catalysis remains elusive. In this study, we discovered that mutations in the structurally buried D38 residue of PP2Cα (PPM1A) redefined the water-mediated hydrogen network in the active site and selectively disrupted M2 metal ion binding. Using the D38A and D38K mutations of PP2Cα as specific tools in combination with enzymology analysis, our results demonstrated that the M2 metal ion determines the rate-limiting step of substrate hydrolysis, participates in dianion substrate binding and stabilizes the leaving group after P-O bond cleavage. The newly characterized catalytic role of the M2 metal ion in this family not only provides insight into how the binuclear metal centers of the PP2C phosphatases are organized for efficient catalysis but also helps increase our understanding of the function and substrate specificity of PP2C family members.


    Organizational Affiliation

    1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Qilu Hospital of Shandong University, Jinan, China [3] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China.,1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China [3] Provincial Hospital affiliated to Shandong University, Jinan, Shandong, China.,Yangtze Delta Region Institute of Tsinghua University, Zhejiang, China.,Department of Human Biology, University of Toronto, Toronto, Ontario, Canada.,1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Qilu Hospital of Shandong University, Jinan, China.,1] Key Laboratory Experimental Teratology of the Ministry of Education and Department of Biochemistry and Molecular Biology, Shandong University, School of Medicine, Jinan, Shandong, China [2] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China.,1] Shandong Provincial School Key laboratory for Protein Science of Chronic Degenerative Diseases, Jinan, Shandong, China [2] Department of Physiology, Shandong University, School of Medicine, Jinan, Shandong, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein phosphatase 1A
A
367Homo 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.199 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 90.817α = 90.00
b = 90.817β = 90.00
c = 105.408γ = 120.00
Software Package:
Software NamePurpose
PHASESphasing
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release