PDBsum entry 3nf3

Hydrolase/hydrolase inhibitor

PDB id: 3nf3

Contents

Protein chain

392 a.a. *

Ligands

ARG-ARG-PHE-AIB-ALA-MET-LEU-ALA

Metals

_NI

_ZN

Waters ×86

* Residue conservation analysis

PDB id:

3nf3

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure of bont/a lc with jth-nb-7239 peptide

Structure:

Bont/a. Chain: a. Fragment: light chain, residues 1-420. Synonym: bont/a1, botulinum neurotoxin type a, neurotoxin a, neurotoxin bont. Engineered: yes. Jth-nb72-39 inhibitor. Chain: c. Engineered: yes

Source:

Clostridium botulinum. Organism_taxid: 1491. Gene: bont/a, bont/a, bonta. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

Resolution:

2.40Å R-factor: 0.185 R-free: 0.231

Authors:

J.E.Zuniga

Key ref:

J.E.Zuniga et al. (2010). Iterative structure-based peptide-like inhibitor design against the botulinum neurotoxin serotype A. Plos One, 5, e11378. PubMed id: 20614028

Date:

09-Jun-10 Release date: 21-Jul-10

Protein chain

Q7B8V4  (Q7B8V4_CLOBO) -  BoNT/A from Clostridium botulinum

Seq: 1296 a.a.

Struc: 392 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.24.69 - bontoxilysin.
• Reaction: Limited hydrolysis of proteins of the neuroexocytosis apparatus, synaptobrevins, SNAP25 or syntaxin. No detected action on small molecule substrates.
• Cofactor: Zn(2+)

Plos One 5:e11378 (2010)

PubMed id: 20614028

Iterative structure-based peptide-like inhibitor design against the botulinum neurotoxin serotype A.

J.E.Zuniga, J.T.Hammill, O.Drory, J.E.Nuss, J.C.Burnett, R.Gussio, P.Wipf, S.Bavari, A.T.Brunger.

ABSTRACT

The botulinum neurotoxin serotype A light chain (BoNT/A LC) protease is the catalytic component responsible for the neuroparalysis that is characteristic of the disease state botulism. Three related peptide-like molecules (PLMs) were designed using previous information from co-crystal structures, synthesized, and assayed for in vitro inhibition against BoNT/A LC. Our results indicate these PLMS are competitive inhibitors of the BoNT/A LC protease and their K(i) values are in the nM-range. A co-crystal structure for one of these inhibitors was determined and reveals that the PLM, in accord with the goals of our design strategy, simultaneously involves both ionic interactions via its P1 residue and hydrophobic contacts by means of an aromatic group in the P2' position. The PLM adopts a helical conformation similar to previously determined co-crystal structures of PLMs, although there are also major differences to these other structures such as contacts with specific BoNT/A LC residues. Our structure further demonstrates the remarkable plasticity of the substrate binding cleft of the BoNT/A LC protease and provides a paradigm for iterative structure-based design and development of BoNT/A LC inhibitors.