3W00

Crystal structure of PcrB complexed with G1P and FsPP from bacillus subtilis subap. subtilis str. 168


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights into TIM-barrel prenyl transferase mechanisms: crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus

Ren, F.Feng, X.Ko, T.P.Huang, C.H.Hu, Y.Chan, H.C.Liu, Y.L.Wang, K.Chen, C.C.Pang, X.He, M.Li, Y.Oldfield, E.Guo, R.T.

(2013) Chembiochem 14: 195-199

  • DOI: 10.1002/cbic.201200748
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Well structured: As a new triose phosphate isomerase (TIM) barrel-fold prenyl transferase, PcrB catalyzes the production of heptaprenylglyceryl phosphate from heptaprenyl diphosphate and glycerol-1-phosphate. Crystal structures of PcrB from Bacillus ...

    Well structured: As a new triose phosphate isomerase (TIM) barrel-fold prenyl transferase, PcrB catalyzes the production of heptaprenylglyceryl phosphate from heptaprenyl diphosphate and glycerol-1-phosphate. Crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus in complex with ligands were solved, and together with site-directed mutagenesis and bioinformatics analyses, clearly reveal the catalytic mechanism of the enzyme.


    Organizational Affiliation

    Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin 300308, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heptaprenylglyceryl phosphate synthase
A, B
228Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: pcrB (yerE)
EC: 2.5.1.n9
Find proteins for O34790 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34790
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FPS
Query on FPS

Download SDF File 
Download CCD File 
B
S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE
FARNESYL THIOPYROPHOSPHATE
C15 H28 O6 P2 S
MYMLCRQRXFRQGP-YFVJMOTDSA-N
 Ligand Interaction
1GP
Query on 1GP

Download SDF File 
Download CCD File 
B
SN-GLYCEROL-1-PHOSPHATE
C3 H9 O6 P
AWUCVROLDVIAJX-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.147α = 90.00
b = 56.392β = 108.15
c = 77.700γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-07-31
    Type: Database references