2ZRW

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with FMN and IPP.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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This is version 1.3 of the entry. See complete history


Literature

New role of flavin as a general acid-base catalyst with no redox function in type 2 isopentenyl-diphosphate isomerase.

Unno, H.Yamashita, S.Ikeda, Y.Sekiguchi, S.Y.Yoshida, N.Yoshimura, T.Kusunoki, M.Nakayama, T.Nishino, T.Hemmi, H.

(2009) J Biol Chem 284: 9160-9167

  • DOI: 10.1074/jbc.M808438200
  • Primary Citation of Related Structures:  
    2ZRZ, 2ZRU, 2ZRV, 2ZRW, 2ZRX, 2ZRY

  • PubMed Abstract: 
  • Using FMN and a reducing agent such as NAD(P)H, type 2 isopentenyl-diphosphate isomerase catalyzes isomerization between isopentenyl diphosphate and dimethylallyl diphosphate, both of which are elemental units for the biosynthesis of highly diverse isoprenoid compounds ...

    Using FMN and a reducing agent such as NAD(P)H, type 2 isopentenyl-diphosphate isomerase catalyzes isomerization between isopentenyl diphosphate and dimethylallyl diphosphate, both of which are elemental units for the biosynthesis of highly diverse isoprenoid compounds. Although the flavin cofactor is expected to be integrally involved in catalysis, its exact role remains controversial. Here we report the crystal structures of the substrate-free and complex forms of type 2 isopentenyl-diphosphate isomerase from the thermoacidophilic archaeon Sulfolobus shibatae, not only in the oxidized state but also in the reduced state. Based on the active-site structures of the reduced FMN-substrate-enzyme ternary complexes, which are in the active state, and on the data from site-directed mutagenesis at highly conserved charged or polar amino acid residues around the active site, we demonstrate that only reduced FMN, not amino acid residues, can catalyze proton addition/elimination required for the isomerase reaction. This discovery is the first evidence for this long suspected, but previously unobserved, role of flavins just as a general acid-base catalyst without playing any redox roles, and thereby expands the known functions of these versatile coenzymes.


    Organizational Affiliation

    Department of Applied Chemistry, Faculty of Engineering, Nagasaki University, Bunkyo-machi, Nagasaki, Nagasaki 852-8521, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isopentenyl-diphosphate delta-isomeraseA, B, C, D368Saccharolobus shibataeMutation(s): 0 
Gene Names: fniidi
EC: 5.3.3.2
Find proteins for P61615 (Saccharolobus shibatae)
Explore P61615 
Go to UniProtKB:  P61615
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.444α = 90
b = 100.444β = 90
c = 333.914γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-05-23
    Changes: Database references
  • Version 1.3: 2013-04-24
    Changes: Non-polymer description