3ZGL

Crystal structures of Escherichia coli IspH in complex with AMBPP a potent inhibitor of the methylerythritol phosphate pathway

• PDB DOI: https://doi.org/10.2210/pdb3ZGL/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli M15
• Mutation(s): No 


• Deposited: 2012-12-18 Released: 2013-01-09 
• Deposition Author(s): Borel, F., Barbier, E., Kratsutsky, S., Janthawornpong, K., Rohmer, M., Dale Poulter, C., Ferrer, J.L., Seemann, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.242 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Further Insight into Crystal Structures of Escherichia coli IspH/LytB in Complex with Two Potent Inhibitors of the MEP Pathway: A Starting Point for Rational Design of New Antimicrobials.

Borel, F., Barbier, E., Krasutsky, S., Janthawornpong, K., Chaignon, P., Poulter, C.D., Ferrer, J.L., Seemann, M.

(2017) Chembiochem 18: 2137-2144

• PubMed: 28862365 
• DOI: https://doi.org/10.1002/cbic.201700363
• Primary Citation of Related Structures:  
  3ZGL, 3ZGN


• PubMed Abstract: 
  

  IspH, also called LytB, a protein involved in the biosynthesis of isoprenoids through the methylerythritol phosphate pathway, is an attractive target for the development of new antimicrobial drugs. Here, we report crystal structures of Escherichia coli IspH in complex with the two most potent inhibitors: (E)-4-mercapto-3-methylbut-2-en-1-yl diphosphate (TMBPP) and (E)-4-amino-3-methylbut-2-en-1-yl diphosphate (AMBPP) at 1.95 and 1.7 Å resolution, respectively. The structure of the E. coli IspH:TMBPP complex exhibited two conformers of the inhibitor. This unexpected feature was exploited to design and evolve new antimicrobial candidates in silico.

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Organizational Affiliation: 

Institut de Biologie Structurale IBS, Université Grenoble Alpes, CEA, CNRS, 38044, Grenoble, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74.5 kDa 
• Atom Count: 5,702 
• Modelled Residue Count: 618 
• Deposited Residue Count: 664 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-HYDROXY-3-METHYLBUT-2-ENYL DIPHOSPHATE REDUCTASE	A, B	332	Escherichia coli	Mutation(s): 0  EC: 1.17.1.2 (PDB Primary Data), 1.17.7.4 (UniProt)
UniProt
Find proteins for P62623 (Escherichia coli (strain K12)) Explore P62623  Go to UniProtKB:  P62623

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	C [auth A], E [auth B]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
10E	D [auth A], F [auth B]	(2E)-4-amino-3-methylbut-2-en-1-yl trihydrogen diphosphate C5 H13 N O7 P2 SZAMOALLMIAULD-GORDUTHDSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.68 Å
• R-Value Free: 0.242 
• R-Value Work: 0.187 
• R-Value Observed: 0.190 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.12	α = 90
b = 80.65	β = 94.63
c = 71.09	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Borel, F., Barbier, E., Kratsutsky, S., Janthawornpong, K., Rohmer, M., Dale Poulter, C., Ferrer, J.L., Seemann, M.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2017-11-29
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description