3ZGN | pdb_00003zgn

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

PDB DOI: https://doi.org/10.2210/pdb3ZGN/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.258 (Depositor), 0.262 (DCC)
R-Value Work:
0.205 (Depositor), 0.210 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201700363
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 74.54 kDa
Atom Count: 5,260
Modeled Residue Count: 618
Deposited Residue Count: 664
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62623
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A]	D [auth A], E [auth B]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth B]
10G Query on 10G Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	(2E)-3-methyl-4-sulfanylbut-2-en-1-yl trihydrogen diphosphate C₅ H₁₂ O₇ P₂ S YSUKJHNOIKPIFM-GORDUTHDSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.258 (Depositor), 0.262 (DCC)
R-Value Work: 0.205 (Depositor), 0.210 (DCC)
R-Value Observed: 0.207 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.39	α = 90
b = 80.57	β = 94.46
c = 70.62	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-01-09

Deposition Author(s):

Revision History (Full details and data files)

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