PDBsum entry 2imc

Hydrolase

PDB id: 2imc

Contents

Protein chains

401 a.a. *

Metals

_ZN ×2

Waters ×426

* Residue conservation analysis

PDB id:

2imc

Name:

Hydrolase

Title:

Clostridium botulinum neurotoxin serotype a light chain, residues 1- 424

Structure:

Botulinum neurotoxin a light-chain. Chain: a, b. Engineered: yes

Source:

Clostridium botulinum. Organism_taxid: 1491. Gene: bota, atx, bna. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.00Å R-factor: 0.198 R-free: 0.230

Authors:

N.R.Silvaggi,K.N.Allen

Key ref:

N.R.Silvaggi et al. (2007). Structures of Clostridium botulinum Neurotoxin Serotype A Light Chain Complexed with Small-Molecule Inhibitors Highlight Active-Site Flexibility. Chem Biol, 14, 533-542. PubMed id: 17524984 DOI: 10.1016/j.chembiol.2007.03.014

Date:

04-Oct-06 Release date: 05-Jun-07

Protein chains

P0DPI1  (BXA1_CLOBH) -  Botulinum neurotoxin type A from Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)

Seq: 1296 a.a.

Struc: 401 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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+)

DOI no: 10.1016/j.chembiol.2007.03.014

Chem Biol 14:533-542 (2007)

PubMed id: 17524984

Structures of Clostridium botulinum Neurotoxin Serotype A Light Chain Complexed with Small-Molecule Inhibitors Highlight Active-Site Flexibility.

N.R.Silvaggi, G.E.Boldt, M.S.Hixon, J.P.Kennedy, S.Tzipori, K.D.Janda, K.N.Allen.

ABSTRACT

The potential for the use of Clostridial neurotoxins as bioweapons makes the development of small-molecule inhibitors of these deadly toxins a top priority. Recently, screening of a random hydroxamate library identified a small-molecule inhibitor of C. botulinum Neurotoxin Serotype A Light Chain (BoNT/A-LC), 4-chlorocinnamic hydroxamate, a derivative of which has been shown to have in vivo efficacy in mice and no toxicity. We describe the X-ray crystal structures of BoNT/A-LC in complexes with two potent small-molecule inhibitors. The structures of the enzyme with 4-chlorocinnamic hydroxamate or 2,4-dichlorocinnamic hydroxamate bound are compared to the structure of the enzyme complexed with L-arginine hydroxamate, an inhibitor with modest affinity. Taken together, this suite of structures provides surprising insights into the BoNT/A-LC active site, including unexpected conformational flexibility at the S1' site that changes the electrostatic environment of the binding pocket. Information gained from these structures will inform the design and optimization of more effective small-molecule inhibitors of BoNT/A-LC.

Selected figure(s)

Figure 2.
Figure 2. Chemical Structures of the Compounds Used in This Study

Figure 4.
Figure 4. Structures of BoNT/A-LC(1–424) Bound to Hydroxamate Inhibitors
Stereo representations of the three enzyme-inhibitor complexes ([A], LC:1; [B], LC:2; [C], LC:3) showing the unweighted 2|F[o]| − |F[c]| simulated annealing composite omit electron-density maps (green mesh) for the inhibitor and residues 366–372 (the 370 loop) contoured at 1.25σ. Active-site residues are represented as cylinders with gray carbon atoms. The inhibitors are shown in ball-and-stick representation with brass carbons. The catalytic Zn(II) ions are rendered as metallic spheres. This figure was rendered using POVScript+ [48] and [49] and POVRAY (www.povray.org).

The above figures are reprinted by permission from Cell Press: Chem Biol (2007, 14, 533-542) copyright 2007.

Figures were selected by an automated process.