Structural analysis of the PP2C Family Phosphatase tPphA from Thermosynechococcus elongatus

Experimental Data Snapshot

  • Resolution: 1.28 Å
  • R-Value Free: 0.204 
  • R-Value Observed: 0.163 

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Structural Analysis of the Pp2C Phosphatase Tppha from Thermosynechococcus Elongatus: A Flexible Flap Subdomain Controls Access to the Catalytic Site.

Schlicker, C.Fokina, O.Kloft, N.Grune, T.Becker, S.Sheldrick, G.M.Forchhammer, K.

(2008) J Mol Biol 376: 570

  • DOI: https://doi.org/10.1016/j.jmb.2007.11.097
  • Primary Citation of Related Structures:  
    2J82, 2J86

  • PubMed Abstract: 

    The homologue of the phosphoprotein PII phosphatase PphA from Thermosynechococcus elongatus, termed tPphA, was identified and its structure was resolved in two different space groups, C222(1) and P4(1)2(1)2, at a resolution of 1.28 and 3.05 A, respectively. tPphA belongs to a large and widely distributed subfamily of Mg(2+)/Mn(2+)-dependent phosphatases of the PPM superfamily characterized by the lack of catalytic and regulatory domains. The core structure of tPphA shows a high degree of similarity to the two PPM structures identified so far. In contrast to human PP2C, but similar to Mycobacterium tuberculosis phosphatase PstP, the catalytic centre exhibits a third metal ion in addition to the dinuclear metal centre universally conserved in all PPM members. The fact that the third metal is only liganded by amino acids, which are universally conserved in all PPM members, implies that the third metal could be general for all members of this family. As a specific feature of tPphA, a flexible subdomain, previously recognized as a flap domain, could be revealed. Comparison of different structural isomers of tPphA as well as site-specific mutagenesis implied that the flap domain is involved in substrate binding and catalytic activity. The structural arrangement of the flap domain was accompanied by a large side-chain movement of an Arg residue (Arg169) at the basis of the flap. Mutation of this residue strongly impaired protein stability as well as catalytic activity, emphasizing the importance of this amino acid for the regional polysterism of the flap subdomain and confirming the assumption that flap domain flexibility is involved in catalysis.

  • Organizational Affiliation

    Department of Structural Chemistry, Georg-August-University, Tammannstrasse 4, 37077 Göttingen, Germany. c_schlicker@yahoo.de

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN SERINE-THREONINE PHOSPHATASE240Synechococcus elongatusMutation(s): 0 
Find proteins for Q8DGS1 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DGS1 
Go to UniProtKB:  Q8DGS1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DGS1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.28 Å
  • R-Value Free: 0.204 
  • R-Value Observed: 0.163 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.216α = 90
b = 151.799β = 90
c = 82.505γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Data collection
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other