Crystal structure of phosphoserine phosphatase from T. onnurineus in complex with NDSB-201

Experimental Data Snapshot

  • Resolution: 1.78 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

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Identification of a Novel Ligand Binding Site in Phosphoserine Phosphatase from the Hyperthermophilic Archaeon Thermococcus Onnurineus.

Jung, T.-Y.S-Kim, Y.Oh, B.H.Woo, E.

(2013) Proteins 81: 819

  • DOI: https://doi.org/10.1002/prot.24238
  • Primary Citation of Related Structures:  
    4AP9, 4B6J

  • PubMed Abstract: 

    Phosphoserine phosphatase (PSP) catalyzes the final and irreversible step of L-serine synthesis by hydrolyzing phosphoserine to produce L-serine and inorganic phosphate. Developing a therapeutic drug that interferes with serine production is of great interest to regulate the pathogenicity of some bacteria and control D-serine levels in neurological diseases. We determined the crystal structure of PSP from the hyperthermophilic archaeon Thermococcus onnurineus at 1.8 Å resolution, revealing an NDSB ligand bound to a novel site that is located in a fissure between the catalytic domain and the CAP module. The structure shows a half-open conformation of the CAP 1 module with a unique protruding loop of residues 150-155 that possesses a helical conformation in other structures of homologous PSPs. Activity assays indicate that the enzyme exhibits marginal PSP activity at low temperature but a sharp increase in the k(cat)/K(M) value, approximately 22 fold, when the temperature is increased. Structural and biochemical analyses suggest that the protruding loop in the active site might be an essential component for the regulation of the activity of PSP from hyperthermophilic T. onnurineus. Identification of this novel binding site distantly located from the catalytic site may be exploited for the development of effective therapeutic allosteric inhibitors against PSP activity.

  • Organizational Affiliation

    Medical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-333, Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
201Thermococcus onnurineusMutation(s): 0 
Find proteins for B6YX36 (Thermococcus onnurineus (strain NA1))
Explore B6YX36 
Go to UniProtKB:  B6YX36
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB6YX36
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.78 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: P 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.131α = 90
b = 128.131β = 90
c = 63.077γ = 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: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Database references