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 
  • R-Value Observed: 0.178 

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This is version 1.3 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: https://doi.org/10.1016/j.febslet.2012.07.070
  • Primary Citation of Related Structures:  
    4G9P

  • 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) 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase406Thermus thermophilus HB27Mutation(s): 0 
Gene Names: gcpEispGTT_C1677
EC: 1.17.7.1
UniProt
Find proteins for Q72H18 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72H18 
Go to UniProtKB:  Q72H18
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ72H18
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
B [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CDI
Query on CDI

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C [auth A]2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE
C5 H12 O9 P2
SFRQRNJMIIUYDI-UHNVWZDZSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
D [auth A],
G [auth A]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
F [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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E [auth A],
H [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.65α = 90
b = 63.65β = 90
c = 442.27γ = 120
Software Package:
Software NamePurpose
SHARPphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations