2Y0F

STRUCTURE OF GCPE (IspG) FROM THERMUS THERMOPHILUS HB27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the E-1-Hydroxy-2-Methyl-But-2-Enyl-4-Diphosphate Synthase (Gcpe) from Thermus Thermophilus.

Rekittke, I.Nonaka, T.Wiesner, J.Demmer, U.Warkentin, E.Jomaa, H.Ermler, U.

(2011) FEBS Lett 585: 447

  • DOI: 10.1016/j.febslet.2010.12.012
  • Primary Citation of Related Structures:  
    2Y0F

  • PubMed Abstract: 
  • Isoprenoids are biosynthesized via the mevalonate or the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways the latter being used by most pathogenic bacteria, some parasitic protozoa, plant plastids, but not by animals. We determined the X-ray structure of the homodimeric [4Fe-4S] cluster carrying E-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate synthase (GcpE) of Thermus thermophilus which catalyzes the penultimate reaction of the MEP pathway and is therefore an attractive target for drug development ...

    Isoprenoids are biosynthesized via the mevalonate or the 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways the latter being used by most pathogenic bacteria, some parasitic protozoa, plant plastids, but not by animals. We determined the X-ray structure of the homodimeric [4Fe-4S] cluster carrying E-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate synthase (GcpE) of Thermus thermophilus which catalyzes the penultimate reaction of the MEP pathway and is therefore an attractive target for drug development. The [4Fe-4S] cluster ligated to three cysteines and one glutamate is encapsulated at the intersubunit interface. The substrate binding site lies in front of an (αβ)(8) barrel. The great [4Fe-4S] cluster-substrate distance implicates large-scale domain rearrangements during the reaction cycle.


    Organizational Affiliation

    Institut für Klinische Immunologie und Transfusionsmedizin, Justus-Liebig-Universität Giessen, Giessen, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
4-HYDROXY-3-METHYLBUT-2-EN-1-YL DIPHOSPHATE SYNTHASEA, B, C, D406Thermus thermophilus HB27Mutation(s): 0 
Gene Names: ispGgcpETT_C1677
EC: 1.17.7.1 (PDB Primary Data), 1.17.7.3 (UniProt)
Find proteins for Q72H18 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72H18 
Go to UniProtKB:  Q72H18
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.5α = 90
b = 130.97β = 102.1
c = 101.26γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
SHARPphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Derived calculations, Other