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TitleStructural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 3027, Year 2024
Publish dateApr 18, 2024
AuthorsAtsushi Yamagata / Kaori Ito / Takehiro Suzuki / Naoshi Dohmae / Tohru Terada / Mikako Shirouzu /
PubMed AbstractMore than one percent of people have epilepsy worldwide. Levetiracetam (LEV) is a successful new-generation antiepileptic drug (AED), and its derivative, brivaracetam (BRV), shows improved efficacy. ...More than one percent of people have epilepsy worldwide. Levetiracetam (LEV) is a successful new-generation antiepileptic drug (AED), and its derivative, brivaracetam (BRV), shows improved efficacy. Synaptic vesicle glycoprotein 2a (SV2A), a putative membrane transporter in the synaptic vesicles (SVs), has been identified as a target of LEV and BRV. SV2A also serves as a receptor for botulinum neurotoxin (BoNT), which is the most toxic protein and has paradoxically emerged as a potent reagent for therapeutic and cosmetic applications. Nevertheless, no structural analysis on AEDs and BoNT recognition by full-length SV2A has been available. Here we describe the cryo-electron microscopy structures of the full-length SV2A in complex with the BoNT receptor-binding domain, BoNT/A2 H and either LEV or BRV. The large fourth luminal domain of SV2A binds to BoNT/A2 H through protein-protein and protein-glycan interactions. LEV and BRV occupy the putative substrate-binding site in an outward-open conformation. A propyl group in BRV creates additional contacts with SV2A, explaining its higher binding affinity than that of LEV, which was further supported by label-free spectral shift assay. Numerous LEV derivatives have been developed as AEDs and positron emission tomography (PET) tracers for neuroimaging. Our work provides a structural framework for AEDs and BoNT recognition of SV2A and a blueprint for the rational design of additional AEDs and PET tracers.
External linksNat Commun / PubMed:38637505 / PubMed Central
MethodsEM (single particle)
Resolution2.82 - 3.38 Å
Structure data

EMDB-36392, PDB-8jlc:
Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and levetiracetam
Method: EM (single particle) / Resolution: 2.88 Å

EMDB-36394, PDB-8jle:
Cryo-EM structure of SV2A LD4 in complex with BoNT/A2 Hc in the SV2A-levetiracetam-BoNT/A2 Hc complex
Method: EM (single particle) / Resolution: 2.82 Å

EMDB-36395, PDB-8jlf:
Cryo-EM structure of SV2A in complex with BoNT/A2 Hc
Method: EM (single particle) / Resolution: 3.01 Å

EMDB-36396, PDB-8jlg:
Cryo-EM structure of SV2A in complex with BoNT/A2 Hc
Method: EM (single particle) / Resolution: 2.87 Å

EMDB-36397, PDB-8jlh:
Cryo-EM structure of SV2A dimer in complex with BoNT/A2 Hc and levetiracetam
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-36398, PDB-8jli:
Cryo-EM structure of SV2A dimer in complex levetiracetam
Method: EM (single particle) / Resolution: 3.38 Å

EMDB-36616, PDB-8js8:
Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and levetiracetam
Method: EM (single particle) / Resolution: 2.88 Å

EMDB-36617, PDB-8js9:
Cryo-EM structure of SV2A in complex with BoNT/A2 Hc
Method: EM (single particle) / Resolution: 3.01 Å

EMDB-36933: Cryo-EM map of SV2A in complex with brivaracetam and BoNT/A2 Hc
Method: EM (single particle) / Resolution: 3.11 Å

EMDB-36934: Local map of SV2A LD4-BoNT/A2 Hc from SV2A-BoNT/A2 Hc-brivaracetam complex
Method: EM (single particle) / Resolution: 3.07 Å

EMDB-36935, PDB-8k77:
Cryo-EM structure of SV2A in complex with BoNT/A2 Hc and brivaracetam
Method: EM (single particle) / Resolution: 3.11 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose


ChemComp, No image

ChemComp-UKX:
Unknown entry


ChemComp, No image

ChemComp-VLX:
Unknown entry

Source
  • homo sapiens (human)
  • clostridium botulinum (bacteria)
KeywordsTRANSPORT PROTEIN / Synaptic vesicle / epilepsy / MEMBRANE PROTEIN / botulinum neurotoxin / Synapse / antiepileptic drug

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