1VG2

Crystal Structure Of Octaprenyl Pyrophosphate Synthase From Hyperthermophilic Thermotoga Maritima A76Y mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.244 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


Literature

A molecular ruler for chain elongation catalyzed by octaprenyl pyrophosphate synthase and its structure-based engineering to produce unprecedented long chain trans-prenyl products

Guo, R.T.Kuo, C.J.Ko, T.P.Chou, C.C.Liang, P.H.Wang, A.H.-J.

(2004) Biochemistry 43: 7678-7686

  • DOI: https://doi.org/10.1021/bi036336d
  • Primary Citation of Related Structures:  
    1VG2, 1VG3, 1VG4, 1VG6, 1VG7

  • PubMed Abstract: 

    Octaprenyl pyrophosphate synthase (OPPs) catalyzes consecutive condensation reactions of farnesyl pyrophosphate (FPP) with five molecules of isopentenyl pyrophosphate (IPP) to generate C(40) octaprenyl pyrophosphate (OPP) which constitutes the side chain of menaquinone. We have previously reported the X-ray structure of OPPs from Thermotoga maritima, which is composed entirely of alpha-helices joined by connecting loops and is arranged with nine core helices around a large central cavity [Guo, R. T., Kuo, C. J., Ko, T. P., Chou, C. C., Shr, R. L., Liang, P. H., and Wang, A. H.-J. (2004) J. Biol. Chem. 279, 4903-4912]. A76 and S77 are located on top of the active site close to where FPP is bound. A76Y and A76Y/S77F OPPs mutants produce C(20), indicating that the substituted larger residues interfere with the substrate chain elongation. Surprisingly, the A76Y/S77F mutant synthesizes a larger amount of C(20) than the A76Y mutant. In the crystal structure of the A76Y/S77F mutant, F77 is pushed away by Y76, thereby creating more space between those two large amino acids to accommodate the C(20) product. A large F132 residue at the bottom of the tunnel-shaped active site serves as the "floor" and determines the final product chain length. The substitution of F132 with a small Ala, thereby removing the blockade, led to the synthesis of a C(50) product larger than that produced by the wild-type enzyme. On the basis of the structure, we have sequentially mutated the large amino acids, including F132, L128, I123, and D62, to Ala underneath the tunnel. The products of the F132A/L128A/I123A/D62A mutant reach C(95), beyond the largest chain length generated by all known trans-prenyltransferases. Further modifications of the enzyme reaction conditions, including new IPP derivatives, may allow the preparation of high-molecular weight polyprenyl products resembling the rubber molecule.


  • Organizational Affiliation

    Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
octoprenyl-diphosphate synthase299Thermotoga maritimaMutation(s): 1 
EC: 2.5.1.11
UniProt
Find proteins for Q9X1M1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1M1 
Go to UniProtKB:  Q9X1M1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1M1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.244 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.392α = 90
b = 151.392β = 90
c = 64.869γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-18
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 2.0: 2021-11-10
    Changes: Atomic model, Database references
  • Version 2.1: 2023-10-25
    Changes: Advisory, Data collection, Derived calculations, Refinement description