Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 27.92 kDa 
• Atom Count: 2161 
• Residue Count: 249 
• Unique protein chains: 1

6NKE

Wild-type GGGPS from Thermoplasma volcanium

• DOI: 10.2210/pdb6NKE/pdb

• Classification: TRANSFERASE
• Organism(s): Thermoplasma volcanium GSS1
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-01-07 Released: 2019-01-23 
• Deposition Author(s): Blank, P.N., Alderfer, K.E., Gillott, B.N., Christianson, D.W., Himmelberger, J.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.204 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 

Literature

Structural studies of geranylgeranylglyceryl phosphate synthase, a prenyltransferase found in thermophilic Euryarchaeota.

Blank, P.N., Barnett, A.A., Ronnebaum, T.A., Alderfer, K.E., Gillott, B.N., Christianson, D.W., Himmelberger, J.A.

(2020) Acta Crystallogr D Struct Biol 76: 542-557

• PubMed: 32496216 
• DOI: 10.1107/S2059798320004878
• Primary Citation of Related Structures:  
  6NKE


• PubMed Abstract: 
  

Archaea are uniquely adapted to thrive in harsh environments, and one of these adaptations involves the archaeal membrane lipids, which are characterized by their isoprenoid alkyl chains connected via ether linkages to glycerol 1-phosphate. The membrane lipids of the thermophilic and acidophilic euryarchaeota Thermoplasma volcanium are exclusively glycerol dibiphytanyl glycerol tetraethers. The first committed step in the biosynthetic pathway of these archaeal lipids is the formation of the ether linkage between glycerol 1-phosphate and geranylgeranyl diphosphate, and is catalyzed by the enzyme geranylgeranylglyceryl phosphate synthase (GGGPS). The 1.72 Å resolution crystal structure of GGGPS from T. volcanium (TvGGGPS) in complex with glycerol and sulfate is reported here. The crystal structure reveals TvGGGPS to be a dimer, which is consistent with the absence of the aromatic anchor residue in helix α5a that is required for hexamerization in other GGGPS homologs; the hexameric quaternary structure in GGGPS is thought to provide thermostability. A phylogenetic analysis of the Euryarchaeota and a parallel ancestral state reconstruction investigated the relationship between optimal growth temperature and the ancestral sequences. The presence of an aromatic anchor residue is not explained by temperature as an ecological parameter. An examination of the active site of the TvGGGPS dimer revealed that it may be able to accommodate longer isoprenoid substrates, supporting an alternative pathway of isoprenoid membrane-lipid synthesis.

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Organizational Affiliation: 

Department of Chemistry and Physics, DeSales University, 2755 Station Avenue, Center Valley, PA 18034, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geranylgeranylglyceryl phosphate synthase	A	252	Thermoplasma volcanium GSS1	Mutation(s): 0  Gene Names: TV0745, TVG0750626 EC: 2.5.1.41
Find proteins for Q97AR4 (Thermoplasma volcanium (strain ATCC 51530 / DSM 4299 / JCM 9571 / NBRC 15438 / GSS1)) Explore Q97AR4  Go to UniProtKB:  Q97AR4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	A	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.204 
• R-Value Work: 0.197 
• R-Value Observed: 0.197 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.761	α = 90
b = 73.761	β = 90
c = 122.6	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-01-07 
• Released Date: 2019-01-23 
Deposition Author(s): Blank, P.N., Alderfer, K.E., Gillott, B.N., Christianson, D.W., Himmelberger, J.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM56838

Revision History 

• Version 1.0: 2019-01-23
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2020-06-17
  Changes: Database references