4S23 | pdb_00004s23

Structure of the GcpE-HMBPP complex from Thermus thermophilius

• PDB DOI: https://doi.org/10.2210/pdb4S23/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-01-19 Released: 2015-03-25 
• Deposition Author(s): Rekittke, I., Warkentin, E., Jomaa, H., Ermler, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.170 (Depositor), 0.156 (DCC) 
• R-Value Work: 
  0.120 (Depositor) 
• R-Value Observed: 
  0.128 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 25660452 
• DOI: https://doi.org/10.1016/j.bbrc.2015.01.088
• Primary Citation Related Structures: 
  4S23


• 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.

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Organizational Affiliation: 
• Universitätsklinikum Gießen und Marburg GmbH, Marburg, Germany; Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.
Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany.
Universitätsklinikum Gießen und Marburg GmbH, Marburg, Germany. Electronic address: [e-mail].
Max-Planck-Institut für Biophysik, Frankfurt am Main, Germany. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.18 kDa 
• Atom Count: 8,524 
• Modeled Residue Count: 810 
• Deposited Residue Count: 812 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase	A, B	406	Thermus thermophilus	Mutation(s): 0  Gene Names: ispG, gcpE EC: 1.17.7.1 (PDB Primary Data), 1.17.7.3 (UniProt)
UniProt
Find proteins for Q5SLI8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SLI8  Go to UniProtKB:  Q5SLI8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	C [auth A], F [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
H6P	E [auth A], H [auth B]	(2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate C5 H12 O8 P2 MDSIZRKJVDMQOQ-GORDUTHDSA-N
MES	D [auth A], G [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.170 (Depositor), 0.156 (DCC) 
• R-Value Work:  0.120 (Depositor) 
• R-Value Observed: 0.128 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.25	α = 90
b = 63.25	β = 90
c = 372.12	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Rekittke, I., Warkentin, E., Jomaa, H., Ermler, E.

Revision History  

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