6JO3

Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Thermoplasma acidophilum in complex with substrate sn-glycerol-1-phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Thermoplasma acidophilum in complex with the substrate sn-glycerol 1-phosphate.

Nemoto, N.Miyazono, K.I.Tanokura, M.Yamagishi, A.

(2019) Acta Crystallogr F Struct Biol Commun 75: 470-479

  • DOI: 10.1107/S2053230X19007453
  • Primary Citation of Related Structures:  
    6JO3

  • PubMed Abstract: 
  • (S)-3-O-Geranylgeranylglyceryl phosphate synthase (GGGPS) catalyzes the initial ether-bond formation between sn-glycerol 1-phosphate (G1P) and geranylgeranyl pyrophosphate to synthesize (S)-3-O-geranylgeranylglyceryl phosphate in the production of an archaeal cell-membrane lipid molecule ...

    (S)-3-O-Geranylgeranylglyceryl phosphate synthase (GGGPS) catalyzes the initial ether-bond formation between sn-glycerol 1-phosphate (G1P) and geranylgeranyl pyrophosphate to synthesize (S)-3-O-geranylgeranylglyceryl phosphate in the production of an archaeal cell-membrane lipid molecule. Archaeal GGGPS proteins are divided into two groups (group I and group II). In this study, the crystal structure of the archaeal group II GGGPS from Thermoplasma acidophilum (TaGGGPS) was determined at 2.35 Å resolution. The structure of TaGGGPS showed that it has a TIM-barrel fold, the third helix of which is disordered (α3*), and that it forms a homodimer, although a pre-existing structure of an archaeal group II GGGPS (from Methanothermobacter thermautotrophicus) showed a hexameric form. The structure of TaGGGPS showed the precise G1P-recognition mechanism of an archaeal group II GGGPS. The structure of TaGGGPS and molecular-dynamics simulation analysis showed fluctuation of the β2-α2, α3* and α5a regions, which is predicted to be important for substrate uptake and/or product release by TaGGGPS.


    Organizational Affiliation

    Department of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Geranylgeranylglyceryl phosphate synthaseA253Thermoplasma acidophilum DSM 1728Mutation(s): 0 
Gene Names: Ta0995
EC: 2.5.1.41
UniProt
Find proteins for Q9HJH3 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore Q9HJH3 
Go to UniProtKB:  Q9HJH3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HJH3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1GP (Subject of Investigation/LOI)
Query on 1GP

Download Ideal Coordinates CCD File 
B [auth A]SN-GLYCEROL-1-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.595α = 90
b = 105.595β = 90
c = 142.498γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-03
    Type: Initial release
  • Version 1.1: 2019-05-15
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-20
    Changes: Database references