4S3C | pdb_00004s3c

IspG in complex with Epoxide Intermediate

• PDB DOI: https://doi.org/10.2210/pdb4S3C/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-01-26 Released: 2015-05-06 
• Deposition Author(s): Quitterer, F., Frank, A., Wang, K., Rao, G., O'Dowd, B., Li, J., Guerra, F., Abdel-Azeim, S., Bacher, A., Eppinger, J., Oldfield, E., Groll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.161 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.121 (DCC) 
• R-Value Observed: 
  0.125 (Depositor) 

Starting Model: experimental

Literature

Atomic-Resolution Structures of Discrete Stages on the Reaction Coordinate of the [Fe4S4] Enzyme IspG (GcpE).

Quitterer, F., Frank, A., Wang, K., Rao, G., O'Dowd, B., Li, J., Guerra, F., Abdel-Azeim, S., Bacher, A., Eppinger, J., Oldfield, E., Groll, M.

(2015) J Mol Biology 427: 2220-2228

• PubMed: 25868383 
• DOI: https://doi.org/10.1016/j.jmb.2015.04.002
• Primary Citation Related Structures: 
  4S38, 4S39, 4S3A, 4S3B, 4S3C, 4S3D, 4S3E, 4S3F


• PubMed Abstract: 
  

  IspG is the penultimate enzyme in non-mevalonate biosynthesis of the universal terpene building blocks isopentenyl diphosphate and dimethylallyl diphosphate. Its mechanism of action has been the subject of numerous studies but remained unresolved due to difficulties in identifying distinct reaction intermediates. Using a moderate reducing agent and an epoxide substrate analogue, we were now able to trap and crystallographically characterize various stages in the IspG-catalyzed conversion of 2-C-methyl-D-erythritol-2,4-cyclo-diphosphate into (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate. In addition, the enzyme's structure was determined in complex with several inhibitors. These results, combined with recent electron paramagnetic resonance data, allowed us to deduce a detailed and complete IspG catalytic mechanism, which describes all stages from initial ring opening to formation of (E)-1-hydroxy-2-methylbut-2-enyl-4-diphosphate via discrete radical and carbanion intermediates. The data presented in this article provide a guide for the design of selective drugs against many prokaryotic and eukaryotic pathogens to which the non-mevalonate pathway is essential for survival and virulence.

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Organizational Affiliation: 
• Center for Integrated Protein Science, Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Garching D-85747, Germany.
Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.
Division of Physical Sciences and Engineering, KAUST Catalysis Center, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia.

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: 45 kDa 
• Atom Count: 3,471 
• Modeled Residue Count: 402 
• Deposited Residue Count: 406 
• 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	406	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: ispG, TTHA0305 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]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
43Q	B [auth A]	(3S)-1,3-dihydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-2-methylbut-2-ylium, carbokation intermediate C5 H13 O9 P2 NBNBDNPPGPBHHB-RXMQYKEDSA-O
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.161 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.121 (DCC) 
• R-Value Observed: 0.125 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.93	α = 90
b = 62.84	β = 127.02
c = 86.2	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Quitterer, F., Frank, A., Wang, K., Rao, G., O'Dowd, B., Li, J., Guerra, F., Abdel-Azeim, S., Bacher, A., Eppinger, J., Oldfield, E., Groll, M.

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2015-07-01
  Changes: Database references
• Version 1.2: 2018-03-07
  Changes: Data collection
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2023-12-06
  Changes: Data collection