PDBsum entry 3fii

Hydrolase, toxin/protein transport

PDB id: 3fii

Contents

Protein chains

403 a.a. *

28 a.a. *

Metals

_ZN

Waters ×151

* Residue conservation analysis

PDB id:

3fii

Name:

Hydrolase, toxin/protein transport

Title:

Crystal structure of clostridium botulinum neurotoxin serotype f catalytic domain with an inhibitor (inh2)

Structure:

Botulinum neurotoxin type f. Chain: a. Fragment: residues 1-419, catalytic domain. Synonym: bont/f (neurotoxin type f). Engineered: yes. Fragment of vesicle-associated membrane protein 2. Chain: b. Fragment: residues 27-58. Synonym: vamp-2, synaptobrevin-2.

Source:

Clostridium botulinum. Organism_taxid: 1491. Gene: bont/f. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: sequence occurs in homo sapiens

Resolution:

2.17Å R-factor: 0.246 R-free: 0.290

Authors:

R.Agarwal,S.Swaminathan

Key ref:

R.Agarwal et al. (2009). Mode of VAMP substrate recognition and inhibition of Clostridium botulinum neurotoxin F. Nat Struct Biol, 16, 789-794. PubMed id: 19543288 DOI: 10.1038/nsmb.1626

Date:

11-Dec-08 Release date: 23-Jun-09

Protein chain

A7GBG3  (BXF_CLOBL) -  Botulinum neurotoxin type F from Clostridium botulinum (strain Langeland / NCTC 10281 / Type F)

Seq: 1278 a.a.

Struc: 403 a.a.

Protein chain

P63027  (VAMP2_HUMAN) -  Vesicle-associated membrane protein 2 from Homo sapiens

Seq: 116 a.a.

Struc: 28 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chain A: 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: 10.1038/nsmb.1626

Nat Struct Biol 16:789-794 (2009)

PubMed id: 19543288

Mode of VAMP substrate recognition and inhibition of Clostridium botulinum neurotoxin F.

R.Agarwal, J.J.Schmidt, R.G.Stafford, S.Swaminathan.

ABSTRACT

Clostridium botulinum neurotoxins (BoNTs) cleave neuronal proteins responsible for neurotransmitter release, causing the neuroparalytic disease botulism. BoNT serotypes B, D, F and G cleave and inactivate vesicle-associated membrane protein (VAMP), each at a unique peptide bond. The specificity of BoNTs depends on the mode of substrate recognition. We have investigated the mechanism of substrate recognition of BoNT F by determining the crystal structures of its complex with two substrate-based inhibitors, VAMP 22-58/Gln58D-cysteine and 27-58/Gln58D-cysteine. The inhibitors bind to BoNT F in the canonical direction (as seen for BoNTs A and E substrates) but are positioned specifically via three major exosites away from the active site. The cysteine sulfur of the inhibitors interacts with the zinc and exists as sulfinic acid in the inhibitor VAMP 27-58/Gln58D-cysteine. Arg133 and Arg171, which form part of two separate exosites, are crucial for substrate binding and catalysis.

Selected figure(s)

Figure 2.
(a) Interactions of active site zinc with inh1 and inh2. BoNT F residues in the BoNT F–inh1 and BoNT F–inh2 complexes, D-Cys and D-Cys-sulfinic acid, are shown in cyan, light gray, orange and green stick model, respectively. Whereas the sulfur of D-Cys in inh1 has one interaction (2.52 Å with zinc, red label), sulfur, OD1 and OD2 of D-Cys sulfinic acid in inh2 have many interactions with the enzyme molecule (blue labels). (b) Interactions of inh1 at and near the BoNT F active site. BoNT F is shown in ribbons (sky blue) and stick model (light gray) and zinc is in sphere model (magenta), whereas inh1 is in green stick model. BoNT F and VAMP residues are labeled in black and blue, respectively. All interactions between BoNT F and VAMP are shown using dashed lines.

Figure 3.
VAMP inhibitor (inh1) is shown in the middle panel in colored secondary-structure boxes (loop, yellow; -strand, cyan; helix, pink). On either side of the middle panel are the enzyme residues (BoNT F–inh1). These interactions are equally applicable for the common residues of inh1 and inh2 with minor differences in distances, except for the interaction between VAMP Asp40 and BoNT F Lys29, which is present only in inh2. The color-coding for enzyme residues is based on their interaction with the VAMP main chain (MC) or side chains (SC), and vice versa. Colors for the VAMP–BoNT F interactions are: MC:SC, pink; MC:MC, blue; SC:SC, cyan; SC:MC, brown. The intra-chain interactions (in violet) of VAMP at exosite 1 have both MC:MC and also hydrophobic SC:SC.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 789-794) copyright 2009.

Figures were selected by an automated process.