Structure of the GcpE-HMBPP complex from Thermus thermophilius

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.128 

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Structure of the GcpE-HMBPP complex from Thermus thermophilius.

Rekittke, I.Warkentin, E.Jomaa, H.Ermler, U.

(2015) Biochem Biophys Res Commun 458: 246-250

  • DOI: https://doi.org/10.1016/j.bbrc.2015.01.088
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Isoprenoid biosynthesis in many bacteria, plant chloroplasts and parasitic protozoa but not in humans proceeds via the mevalonate independent 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway. Its penultimate reaction step is catalyzed by (E)-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate (HMBPP) synthase (GcpE/IspG) which transforms 2-C-methyl-D-erythritol-2, 4-cyclo-diphosphate (MEcPP) to HMBPP. In this report we present the structure of GcpE of Thermus thermophiles in complex with its product HMBPP at a resolution of 1.65 Å. The GcpE-HMBPP like the GcpE-MEcPP structure is found in a closed, the ligand-free GcpE structure in an open enzyme state. Imposed by the rigid protein scaffold inside the active site funnel, linear HMBPP and circular MEcPP adopt highly similar conformations. The confined space also determines the conformational freedom of transition state intermediates and the design of anti-infective drugs. The apical Fe of the [4Fe-4S] cluster is coordinated to MEcPP in the GcpE-MEcPP complex and to a hydroxyl/water ligand but not to HMBPP in the GcpE-HMBPP complex. The GcpE-HMBPP structure can be attributed to one step in the currently proposed GcpE reaction cycle.

  • Organizational Affiliation

    Universitätsklinikum Gießen und Marburg GmbH, Marburg, Germany; Max-Planck-Institut für Biophysik, Frankfurt am Main, 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
406Thermus thermophilusMutation(s): 0 
Gene Names: ispGgcpE
Find proteins for Q5SLI8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SLI8 
Go to UniProtKB:  Q5SLI8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SLI8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.128 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.25α = 90
b = 63.25β = 90
c = 372.12γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-25
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description