6EMI | pdb_00006emi

Crystal structure of a variant of human butyrylcholinesterase expressed in bacteria.

PDB DOI: https://doi.org/10.2210/pdb6EMI/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2017-10-02 Released: 2017-11-08
Deposition Author(s): Brazzolotto, X., Igert, A., Guillon, V., Santoni, G., Nachon, F.
Funding Organization(s): French Ministry of Defense

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free:
0.255 (Depositor), 0.261 (DCC)
R-Value Work:
0.222 (Depositor), 0.228 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Bacterial Expression of Human Butyrylcholinesterase as a Tool for Nerve Agent Bioscavengers Development.

Brazzolotto, X., Igert, A., Guillon, V., Santoni, G., Nachon, F.

(2017) Molecules 22

PubMed: 29077024 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/molecules22111828
Primary Citation Related Structures:
6EMI

PubMed Abstract:
Human butyrylcholinesterase is a performant stoichiometric bioscavenger of organophosphorous nerve agents. It is either isolated from outdated plasma or functionally expressed in eukaryotic systems. Here, we report the production of active human butyrylcholinesterase in a prokaryotic system after optimization of the primary sequence through the Protein Repair One Stop Shop process, a structure- and sequence-based algorithm for soluble bacterial expression of difficult eukaryotic proteins. The mutant enzyme was purified to homogeneity. Its kinetic parameters with substrate are similar to the endogenous human butyrylcholinesterase or recombinants produced in eukaryotic systems. The isolated protein was prone to crystallize and its 2.5-Å X-ray structure revealed an active site gorge region identical to that of previously solved structures. The advantages of this alternate expression system, particularly for the generation of butyrylcholinesterase variants with nerve agent hydrolysis activity, are discussed.

Organizational Affiliation

Institut de Recherche Biomédicale des Armées, Département de Toxicologie et Risques Chimiques, 1 Place Général Valérie André, 91223 Brétigny-sur-Orge, France. xavier@brazzolotto.net.

Macromolecule Content

Total Structure Weight: 123.73 kDa
Atom Count: 9,018
Modeled Residue Count: 1,054
Deposited Residue Count: 1,064
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinesterase	A, B	532	Homo sapiens	Mutation(s): 47 Gene Names: BCHE, CHE1 EC: 3.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P06276 (Homo sapiens) Explore P06276 Go to UniProtKB: P06276
PHAROS: P06276 GTEx: ENSG00000114200
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06276
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain OA [auth B] SDF format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain NA [auth B]	NA [auth B], OA [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain NA [auth B] Focus chain OA [auth B] Interactions & Density Focus chain NA [auth B] Focus chain OA [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain LA [auth B] SDF format, chain L [auth A] SDF format, chain KA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B]	KA [auth B] L [auth A] LA [auth B] M [auth A] MA [auth B] KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], O [auth A], P [auth A], Q [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain F [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth A]	F [auth A], FA [auth B], GA [auth B], HA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Interactions & Density Focus chain F [auth A] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain EA [auth B] SDF format, chain E [auth A] SDF format, chain DA [auth B] SDF format, chain D [auth A] SDF format, chain CA [auth B] SDF format, chain C [auth A] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain C [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain C [auth A] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] C [auth A] CA [auth B] D [auth A] AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain J [auth A] SDF format, chain IA [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] IA [auth B] J [auth A] G [auth A], H [auth A], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.48 Å
R-Value Free: 0.255 (Depositor), 0.261 (DCC)
R-Value Work: 0.222 (Depositor), 0.228 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.84	α = 90
b = 75.17	β = 93.37
c = 122.07	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
autoPROC	data scaling
MxCuBE	data collection
autoPROC	data reduction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-11-08

Deposition Author(s):

Funding Organization	Location	Grant Number
French Ministry of Defense	France	PDH-2-NRBC-3-C-3201

Revision History (Full details and data files)

Version 1.0: 2017-11-08
Type: Initial release
Version 1.1: 2024-01-17
Changes: Advisory, Data collection, Database references, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary