Crystal structure of Octaprenyl Pyrophosphate synthase from Escherichia coli

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.228 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


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.

(2015) Proteins 83: 37-45

  • DOI: https://doi.org/10.1002/prot.24618
  • Primary Citation of Related Structures:  
    3WJK, 3WJN, 3WJO

  • 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, 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Octaprenyl diphosphate synthase
A, B
337Escherichia coli O104:H4 str. 2009EL-2071Mutation(s): 0 
Gene Names: O3O_22640
EC: 2.5.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 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
b = 128.39β = 90
c = 46.385γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Refinement description