4AQD | pdb_00004aqd

Crystal structure of fully glycosylated human butyrylcholinesterase

PDB DOI: https://doi.org/10.2210/pdb4AQD/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Drosophila melanogaster
Mutation(s): No

Deposited: 2012-04-16 Released: 2012-07-04
Deposition Author(s): Brazzolotto, X., Wandhammer, M., Ronco, C., Trovaslet, M., Jean, L., Lockridge, O., Renard, P.Y., Nachon, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.163 (Depositor), 0.164 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

Human butyrylcholinesterase produced in insect cells: huprine-based affinity purification and crystal structure.

Brazzolotto, X., Wandhammer, M., Ronco, C., Trovaslet, M., Jean, L., Lockridge, O., Renard, P.Y., Nachon, F.

(2012) FEBS J 279: 2905-2916

PubMed: 22726956 Search on PubMed
DOI: https://doi.org/10.1111/j.1742-4658.2012.08672.x
Primary Citation Related Structures:
4AQD

PubMed Abstract:
Butyrylcholinesterase (BChE) is a serine hydrolase that is present in all mammalian tissues. It can accommodate larger substrates or inhibitors than acetylcholinesterase (AChE), the enzyme responsible for hydrolysis of the neurotransmitter acetylcholine in the central nervous system and neuromuscular junctions. AChE is the specific target of organophosphorous pesticides and warfare nerve agents, and BChE is a stoichiometric bioscavenger. Conversion of BChE into a catalytic bioscavenger by rational design or designing reactivators specific to BChE required structural data obtained using a recombinant low-glycosylated human BChE expressed in Chinese hamster ovary cells. This expression system yields ≈ 1 mg of pure enzyme per litre of cell culture. Here, we report an improved expression system using insect cells with a fourfold higher yield for truncated human BChE with all glycosylation sites present. We developed a fast purification protocol for the recombinant protein using huprine-based affinity chromatography, which is superior to the classical procainamide-based affinity. The purified BChE crystallized under different conditions and space group than the recombinant low-glycosylated protein produced in Chinese hamster ovary cells. The crystals diffracted to 2.5 Å. The overall monomer structure is similar to the low-glycosylated structure except for the presence of the additional glycans. Remarkably, the carboxylic acid molecule systematically bound to the catalytic serine in the low-glycosylated structure is also present in this new structure, despite the different expression system, purification protocol and crystallization conditions.

Organizational Affiliation

Département de Toxicologie, Institut de Recherche Biomédicale des Armées, La Tronche, France. xavier@brazzolotto.net

Macromolecule Content

Total Structure Weight: 128.35 kDa
Atom Count: 9,253
Modeled Residue Count: 1,053
Deposited Residue Count: 1,062
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BUTYRYLCHOLINESTERASE	A, B	531	Homo sapiens	Mutation(s): 0 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
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P06276-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	2		N-Glycosylation	Interactions Focus chain C Focus chain E Interactions & Density Focus chain C Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D, F, H, I, J D, F, H, I, J, K	3		N-Glycosylation	Interactions Focus chain D Focus chain F Focus chain H Focus chain I Focus chain J Focus chain K Interactions & Density Focus chain D Focus chain F Focus chain H Focus chain I Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G28454KX GlyCosmos: G28454KX GlyGen: G28454KX

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	3		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain JA [auth B] mmCIF format, chain KA [auth B] mmCIF format, chain LA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B]	IA [auth B] JA [auth B] KA [auth B] LA [auth B] M [auth A] IA [auth B], JA [auth B], KA [auth B], LA [auth B], M [auth A], MA [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A]	N [auth A], O [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain N [auth A] Focus chain O [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain NA [auth B] SDF format, chain OA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B]	NA [auth B], OA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-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]
BAL Query on BAL Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain HA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain HA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain HA [auth B]	HA [auth B], L [auth A]	BETA-ALANINE C₃ H₇ N O₂ UCMIRNVEIXFBKS-UHFFFAOYSA-N		Interactions Focus chain HA [auth B] Focus chain L [auth A] Interactions & Density Focus chain HA [auth B] Focus chain L [auth A]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain IB [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain IB [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain IB [auth B]	GA [auth A], IB [auth B]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain GA [auth A] Focus chain IB [auth B] Interactions & Density Focus chain GA [auth A] Focus chain IB [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain XA [auth B] SDF format, chain YA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth B] MOL2 format, chain YA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth B] mmCIF format, chain YA [auth B]	P [auth A] PA [auth B] Q [auth A] QA [auth B] R [auth A] P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], YA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain YA [auth B] Interactions & Density Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain YA [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain DA [auth A] SDF format, chain DB [auth B] SDF format, chain EA [auth A] SDF format, chain EB [auth B] SDF format, chain GB [auth B] SDF format, chain HB [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain DB [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain EB [auth B] MOL2 format, chain GB [auth B] MOL2 format, chain HB [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain DB [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain EB [auth B] mmCIF format, chain GB [auth B] mmCIF format, chain HB [auth B]	CA [auth A] DA [auth A] DB [auth B] EA [auth A] EB [auth B] CA [auth A], DA [auth A], DB [auth B], EA [auth A], EB [auth B], GB [auth B], HB [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth A] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain GB [auth B] Focus chain HB [auth B] Interactions & Density Focus chain CA [auth A] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain GB [auth B] Focus chain HB [auth B]
UNX Query on UNX Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain BA [auth A] SDF format, chain BB [auth B] SDF format, chain CB [auth B] SDF format, chain FA [auth A] SDF format, chain FB [auth B] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain BA [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain CB [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain FB [auth B] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain BA [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain CB [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain FB [auth B] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B]	AA [auth A] AB [auth B] BA [auth A] BB [auth B] CB [auth B] AA [auth A], AB [auth B], BA [auth A], BB [auth B], CB [auth B], FA [auth A], FB [auth B], Y [auth A], Z [auth A], ZA [auth B]	UNKNOWN ATOM OR ION X		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain BA [auth A] Focus chain BB [auth B] Focus chain CB [auth B] Focus chain FA [auth A] Focus chain FB [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Focus chain ZA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.163 (Depositor), 0.164 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.75	α = 90
b = 79.26	β = 90
c = 227.2	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-07-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-07-04
Type: Initial release
Version 1.1: 2012-08-08
Changes: Database references
Version 1.2: 2013-11-20
Changes: Derived calculations
Version 1.3: 2018-11-14
Changes: Advisory, Data collection, Database references
Version 1.4: 2019-03-06
Changes: Data collection, Derived calculations, Experimental preparation
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary