6JO3

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

Replaces:  5B69

Summary for 6JO3

• Entry DOI: 10.2210/pdb6jo3/pdb
• Related: 2f6x 4mm1
• Descriptor: Geranylgeranylglyceryl phosphate synthase, SN-GLYCEROL-1-PHOSPHATE (3 entities in total)
• Functional Keywords: archaea, ether lipid, thermoplasma, transferase, structural genomics
• Biological source: Thermoplasma acidophilum DSM 1728
• Total number of polymer chains: 1
• Total formula weight: 27455.84

Authors

Nemoto, N.,Miyazono, K.,Tanokura, M.,Yamagishi, A. (deposition date: 2019-03-20, release date: 2019-04-03, Last modification date: 2023-11-22)

Primary citation

Nemoto, N.,Miyazono, K.I.,Tanokura, M.,Yamagishi, A.
Crystal structure of (S)-3-O-geranylgeranylglyceryl phosphate synthase from Thermoplasma acidophilum in complex with the substrate sn-glycerol 1-phosphate.
Acta Crystallogr.,Sect.F, 75:470-479, 2019

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.

PubMed: 31282866
DOI: 10.1107/S2053230X19007453

Experimental method

X-RAY DIFFRACTION (2.35 Å)