4MM1

GGGPS from Methanothermobacter thermautotrophicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8004 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A comprehensive analysis of the geranylgeranylglyceryl phosphate synthase enzyme family identifies novel members and reveals mechanisms of substrate specificity and quaternary structure organization.

Peterhoff, D.Beer, B.Rajendran, C.Kumpula, E.P.Kapetaniou, E.Guldan, H.Wierenga, R.K.Sterner, R.Babinger, P.

(2014) Mol.Microbiol. 92: 885-899

  • DOI: 10.1111/mmi.12596
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Geranylgeranylglyceryl phosphate synthase (GGGPS) family enzymes catalyse the formation of an ether bond between glycerol-1-phosphate and polyprenyl diphosphates. They are essential for the biosynthesis of archaeal membrane lipids, but also occur in ...

    Geranylgeranylglyceryl phosphate synthase (GGGPS) family enzymes catalyse the formation of an ether bond between glycerol-1-phosphate and polyprenyl diphosphates. They are essential for the biosynthesis of archaeal membrane lipids, but also occur in bacterial species, albeit with unknown physiological function. It has been known that there exist two phylogenetic groups (I and II) of GGGPS family enzymes, but a comprehensive study has been missing. We therefore visualized the variability within the family by applying a sequence similarity network, and biochemically characterized 17 representative GGGPS family enzymes regarding their catalytic activities and substrate specificities. Moreover, we present the first crystal structures of group II archaeal and bacterial enzymes. Our analysis revealed that the previously uncharacterized bacterial enzymes from group II have GGGPS activity like the archaeal enzymes and differ from the bacterial group I enzymes that are heptaprenylglyceryl phosphate synthases. The length of the isoprenoid substrate is determined in group II GGGPS enzymes by 'limiter residues' that are different from those in group I enzymes, as shown by site-directed mutagenesis. Most of the group II enzymes form hexamers. We could disrupt these hexamers to stable and catalytically active dimers by mutating a single amino acid that acts as an 'aromatic anchor'.


    Organizational Affiliation

    Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, 93040, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Geranylgeranylglyceryl phosphate synthase
A, B, C, D, E, F
250Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)Mutation(s): 0 
EC: 2.5.1.41
Find proteins for O26652 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Go to UniProtKB:  O26652
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download SDF File 
Download CCD File 
A, B, C, D, E, F
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
1GP
Query on 1GP

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SN-GLYCEROL-1-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8004 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.675α = 90.00
b = 148.756β = 109.50
c = 91.503γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
XDSdata reduction
PHENIXmodel building
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description