Crystal structure of Pyrococcus horikoshii mannosyl-3-phosphoglycerate phosphatase complexed with MG2+ and phosphate

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.219 

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Structure of mannosyl-3-phosphoglycerate phosphatase from Pyrococcus horikoshii.

Kawamura, T.Watanabe, N.Tanaka, I.

(2008) Acta Crystallogr D Biol Crystallogr 64: 1267-1276

  • DOI: https://doi.org/10.1107/S0907444908033817
  • Primary Citation of Related Structures:  
    1WZC, 2ZOS

  • PubMed Abstract: 

    Mannosyl-3-phosphoglycerate phosphatase (MPGP) catalyzes the dephosphorylation of alpha-mannosyl-3-phosphoglycerate (MPG) to produce alpha-mannosylglycerate (MG). In the hyperthermophile Pyrococcus horikoshii, MPGP plays a role in a series of enzyme reactions that are involved in the MG-biosynthesis pathway, which is important for maintaining life under conditions of high salt concentration. Crystal structures of P. horikoshii MPGP (PhoMPGP) in the holo form and in the apo form lacking the magnesium ion were determined by the multiple-wavelength anomalous diffraction method using SeMet-substituted PhoMPGP. PhoMPGP consists of two domains: a core domain that is conserved in the haloacid dehalogenase superfamily and a cap domain that is specific to the C2B cap subclass of the superfamily. Apo-form crystals contain two PhoMPGP molecules: one in the open conformation and the other in the closed conformation. In holo-form crystals both of the two molecules are in the closed conformation with phosphate and magnesium ions. PhoMPGP has a specific hairpin loop that is bent towards the active site in the closed conformation of both the apo and holo forms. PhoMPGP has a cavity between the two domains which is considered to be the substrate-binding site as a phosphate ion is located in the cavity, mimicking the binding manner of the phosphate group of MPG. The cavity is sequestered in the closed conformation such that a conformational change is indispensable for the release of products. A salt bridge from the general acid/base Asp10 to Arg170 is observed in the holo-form PhoMPGP which is not present in the open form. The importance of the conformational change in the activity of PhoMPGP is discussed.

  • Organizational Affiliation

    Division of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0810, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mannosyl-3-phosphoglycerate phosphatase
A, B
249Pyrococcus horikoshiiMutation(s): 1 
Gene Names: PH0926
Find proteins for O58690 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O58690 
Go to UniProtKB:  O58690
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO58690
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.219 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.833α = 90
b = 70.691β = 98.15
c = 67.911γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-03-06
    Changes: Other
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-05-29
    Changes: Data collection