Crystal structure of Tk-PTP in the G95A mutant form

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

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Structural study reveals the temperature-dependent conformational flexibility of Tk-PTP, a protein tyrosine phosphatase from Thermococcus kodakaraensis KOD1

Yun, H.Y.Lee, J.Kim, H.Ryu, H.Shin, H.C.Oh, B.H.Ku, B.Kim, S.J.

(2018) PLoS One 13: e0197635-e0197635

  • DOI: https://doi.org/10.1371/journal.pone.0197635
  • Primary Citation of Related Structures:  
    5Z59, 5Z5A, 5Z5B

  • PubMed Abstract: 

    Protein tyrosine phosphatases (PTPs) originating from eukaryotes or bacteria have been under intensive structural and biochemical investigation, whereas archaeal PTP proteins have not been investigated extensively; therefore, they are poorly understood. Here, we present the crystal structures of Tk-PTP derived from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1, in both the active and inactive forms. Tk-PTP adopts a common dual-specificity phosphatase (DUSP) fold, but it undergoes an atypical temperature-dependent conformational change in its P-loop and α4-α5 loop regions, switching between the inactive and active forms. Through comprehensive analyses of Tk-PTP, including additional structural determination of the G95A mutant form, enzymatic activity assays, and structural comparison with the other archaeal PTP, it was revealed that the presence of the GG motif in the P-loop is necessary but not sufficient for the structural flexibility of Tk-PTP. It was also proven that Tk-PTP contains dual general acid/base residues unlike most of the other DUSP proteins, and that both the residues are critical in its phosphatase activity. This work provides the basis for expanding our understanding of the previously uncharacterized PTP proteins from archaea, the third domain of living organisms.

  • Organizational Affiliation

    Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-tyrosine phosphatase
A, B, C
160Thermococcus kodakarensis KOD1Mutation(s): 1 
Gene Names: Tk-ptpTK0241
Find proteins for Q8X270 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore Q8X270 
Go to UniProtKB:  Q8X270
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8X270
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.796α = 90
b = 154.796β = 90
c = 75.24γ = 120
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: 2018-06-27
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description