4NAF

PrcB from Geobacillus kaustophilus, apo structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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:  
    4NAE, 4NAF, 4MM1, 4JEJ

  • 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 bacterial species, albeit with unknown physiological function ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heptaprenylglyceryl phosphate synthaseA226Geobacillus kaustophilus HTA426Mutation(s): 0 
Gene Names: pcrBGK0274
EC: 2.5.1
Find proteins for Q5L3C1 (Geobacillus kaustophilus (strain HTA426))
Explore Q5L3C1 
Go to UniProtKB:  Q5L3C1
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Heptaprenylglyceryl phosphate synthaseB227Geobacillus kaustophilus HTA426Mutation(s): 0 
Gene Names: pcrBGK0274
EC: 2.5.1
Find proteins for Q5L3C1 (Geobacillus kaustophilus (strain HTA426))
Explore Q5L3C1 
Go to UniProtKB:  Q5L3C1
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.114α = 90
b = 157.84β = 90
c = 38.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-25
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Data collection