4G9P

Structure of the GcpE-MEcPP (IspG) complex from Thermus thermophilus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the GcpE (IspG)-MEcPP complex from Thermus thermophilus.

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

(2012) Febs Lett. 586: 3452-3457

  • DOI: 10.1016/j.febslet.2012.07.070

  • PubMed Abstract: 
  • Isoprenoid precursor biosynthesis occurs through the mevalonate or the methylerythritol phosphate (MEP) pathway, used i.e., by humans and by many human pathogens, respectively. In the MEP pathway, 2-C-methyl-D-erythritol-2,4-cyclo-diphosphate (MEcPP) ...

    Isoprenoid precursor biosynthesis occurs through the mevalonate or the methylerythritol phosphate (MEP) pathway, used i.e., by humans and by many human pathogens, respectively. In the MEP pathway, 2-C-methyl-D-erythritol-2,4-cyclo-diphosphate (MEcPP) is converted to (E)-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate (HMBPP) by the iron-sulfur cluster enzyme HMBPP synthase (GcpE). The presented X-ray structure of the GcpE-MEcPP complex from Thermus thermophilus at 1.55Å resolution provides valuable information about the catalytic mechanism and for rational inhibitor design. MEcPP binding inside the TIM-barrel funnel induces a 60° rotation of the [4Fe-4S] cluster containing domain onto the TIM-barrel entrance. The apical iron of the [4Fe-4S] cluster ligates with the C3 oxygen atom of MEcPP.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase
A
406Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: ispG (gcpE)
EC: 1.17.7.3
Find proteins for Q72H18 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72H18
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

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Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CDI
Query on CDI

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Download CCD File 
A
2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
C5 H12 O9 P2
SFRQRNJMIIUYDI-UHNVWZDZSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.177 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 63.650α = 90.00
b = 63.650β = 90.00
c = 442.270γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
SHARPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2012-10-17
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description