6JO3 | pdb_00006jo3

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

• PDB DOI: https://doi.org/10.2210/pdb6JO3/pdb
• Entry: 6JO3 supersedes: 5B69

• Classification: TRANSFERASE
• Organism(s): Thermoplasma acidophilum DSM 1728
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-03-20 Released: 2019-04-03 
• Deposition Author(s): Nemoto, N., Miyazono, K., Tanokura, M., Yamagishi, A.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

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

• PubMed: 31282866 
• DOI: https://doi.org/10.1107/S2053230X19007453
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Faculty of Advanced Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan.
Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
Department of Life Science, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 27.46 kDa 
• Atom Count: 1,913 
• Modeled Residue Count: 247 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranylglyceryl phosphate synthase	A	253	Thermoplasma acidophilum DSM 1728	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1GP (Subject of Investigation/LOI)	B [auth A]	SN-GLYCEROL-1-PHOSPHATE C3 H9 O6 P AWUCVROLDVIAJX-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.595	α = 90
b = 105.595	β = 90
c = 142.498	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Nemoto, N., Miyazono, K., Tanokura, M., Yamagishi, A.
• This entry supersedes: 5B69

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	--

Revision History  

• 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
• Version 1.4: 2023-11-22
  Changes: Data collection, Database references, Refinement description