PDBsum entry 5fpp

Hydrolase

PDB id: 5fpp

Contents

Protein chains

541 a.a.

Ligands

NAG

CO3 ×2

P6G

AE3 ×2

HI6 ×2

Waters ×457

PDB id:

5fpp

Name:

Hydrolase

Title:

Structure of a pre-reaction ternary complex between sarin- acetylcholinesterase and hi-6

Structure:

Acetylcholinesterase. Chain: a, b. Fragment: catalytic domain, unp residues 32-574. Synonym: ache. Engineered: yes. Other_details: sarin phosphonylation product covalently attached to ser203

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek293f

Resolution:

2.40Å R-factor: 0.176 R-free: 0.213

Authors:

A.Allgardsson,L.Berg,C.Akfur,A.Hornberg,F.Worek,A.Linusson,F.Ekstrom

Key ref:

A.Allgardsson et al. (2016). Structure of a prereaction complex between the nerve agent sarin, its biological target acetylcholinesterase, and the antidote HI-6. Proc Natl Acad Sci U S A, 113, 5514-5519. PubMed id: 27140636 DOI: 10.1073/pnas.1523362113

Date:

02-Dec-15 Release date: 11-May-16

Protein chains

P21836  (ACES_MOUSE) -  Acetylcholinesterase from Mus musculus

Seq: 614 a.a.

Struc: 541 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.1.7 - acetylcholinesterase.
• Reaction: acetylcholine + H2O = choline + acetate + H⁺

acetylcholine (Bound ligand (Het Group name = NAG) matches with 41.18% similarity) + H2O = choline (Bound ligand (Het Group name = CO3) matches with 60.00% similarity) + acetate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1073/pnas.1523362113

Proc Natl Acad Sci U S A 113:5514-5519 (2016)

PubMed id: 27140636

Structure of a prereaction complex between the nerve agent sarin, its biological target acetylcholinesterase, and the antidote HI-6.

A.Allgardsson, L.Berg, C.Akfur, A.Hörnberg, F.Worek, A.Linusson, F.J.Ekström.

ABSTRACT

Organophosphorus nerve agents interfere with cholinergic signaling by covalently binding to the active site of the enzyme acetylcholinesterase (AChE). This inhibition causes an accumulation of the neurotransmitter acetylcholine, potentially leading to overstimulation of the nervous system and death. Current treatments include the use of antidotes that promote the release of functional AChE by an unknown reactivation mechanism. We have used diffusion trap cryocrystallography and density functional theory (DFT) calculations to determine and analyze prereaction conformers of the nerve agent antidote HI-6 in complex with Mus musculus AChE covalently inhibited by the nerve agent sarin. These analyses reveal previously unknown conformations of the system and suggest that the cleavage of the covalent enzyme-sarin bond is preceded by a conformational change in the sarin adduct itself. Together with data from the reactivation kinetics, this alternate conformation suggests a key interaction between Glu202 and the O-isopropyl moiety of sarin. Moreover, solvent kinetic isotope effect experiments using deuterium oxide reveal that the reactivation mechanism features an isotope-sensitive step. These findings provide insights into the reactivation mechanism and provide a starting point for the development of improved antidotes. The work also illustrates how DFT calculations can guide the interpretation, analysis, and validation of crystallographic data for challenging reactive systems with complex conformational dynamics.