Crystal structure of IspG (gcpE)

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 

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Biosynthesis of isoprenoids: crystal structure of the [4Fe-4S] cluster protein IspG.

Lee, M.Grawert, T.Quitterer, F.Rohdich, F.Eppinger, J.Eisenreich, W.Bacher, A.Groll, M.

(2010) J Mol Biol 404: 600-610

  • DOI: https://doi.org/10.1016/j.jmb.2010.09.050
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    IspG protein serves as the penultimate enzyme of the recently discovered non-mevalonate pathway for the biosynthesis of the universal isoprenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate. The enzyme catalyzes the reductive ring opening of 2C-methyl-D-erythritol 2,4-cyclodiphosphate, which affords 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. The protein was crystallized under anaerobic conditions, and its three-dimensional structure was determined to a resolution of 2.7 Å. Each subunit of the c(2) symmetric homodimer folds into two domains connected by a short linker sequence. The N-terminal domain (N domain) is an eight-stranded β barrel that belongs to the large TIM-barrel superfamily. The C-terminal domain (C domain) consists of a β sheet that is flanked on both sides by helices. One glutamate and three cysteine residues of the C domain coordinate a [4Fe-4S] cluster. Homodimer formation involves an extended contact area (about 1100 Å(2)) between helices 8 and 9 of each respective β barrel. Moreover, each C domain contacts the N domain of the partner subunit, but the interface regions are small (about 430 Å(2)). We propose that the enzyme substrate binds to the positively charged surface area at the C-terminal pole of the β barrel. The C domain carrying the iron-sulfur cluster could then move over to form a closed conformation where the substrate is sandwiched between the N domain and the C domain. This article completes the set of three-dimensional structures of the non-mevalonate pathway enzymes, which are of specific interest as potential targets for tuberculostatic and antimalarial drugs.

  • Organizational Affiliation

    Lehrstuhl für Biochemie, Center for Integrated Protein Science Munich, Department Chemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
A, B, C, D
366Aquifex aeolicusMutation(s): 0 
Gene Names: aq_1540gcpEispG
EC: (PDB Primary Data), (UniProt)
Find proteins for O67496 (Aquifex aeolicus (strain VF5))
Explore O67496 
Go to UniProtKB:  O67496
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67496
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.224 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 243.7α = 90
b = 119.01β = 95.48
c = 63.82γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-10-09
    Changes: Database references