3WJK

Crystal structure of Octaprenyl Pyrophosphate synthase from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structures of ligand-bound octaprenyl pyrophosphate synthase from escherichia coli reveal the catalytic and chain-length determining mechanisms

Han, X.Chen, C.C.Kuo, C.J.Huang, C.H.Zheng, Y.Ko, T.P.Zhu, Z.Feng, X.Wang, K.Oldfield, E.Wang, A.H.Liang, P.H.Guo, R.T.Ma, Y.

(2014) Proteins --: --

  • DOI: 10.1002/prot.24618
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of one allylic substrate farnesyl pyrophosphate (FPP) and five homoallylic substrate isopentenyl pyrophosphate (IPP) molecules to form a C40 long-chain product OPP, ...

    Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of one allylic substrate farnesyl pyrophosphate (FPP) and five homoallylic substrate isopentenyl pyrophosphate (IPP) molecules to form a C40 long-chain product OPP, which serves as a side chain of ubiquinone and menaquinone. OPPs belongs to the trans-prenyltransferase class of proteins. The structures of OPPs from Escherichia coli were solved in the apo-form as well as in complexes with IPP and a FPP thio-analog, FsPP, at resolutions of 2.2-2.6 Å, and revealed the detailed interactions between the ligands and enzyme. At the bottom of the active-site tunnel, M123 and M135 act in concert to form a wall which determines the final chain length. These results represent the first ligand-bound crystal structures of a long-chain trans-prenyltransferase and provide new information on the mechanisms of catalysis and product chain elongation.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Octaprenyl diphosphate synthase
A, B
337N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 116.946α = 90.00
b = 128.390β = 90.00
c = 46.385γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release