PDBsum entry 3gcd

Toxin/inhibitor

PDB id: 3gcd

Contents

Protein chains

202 a.a. *

Ligands

AZ0 ×4

IHP ×4

Metals

_NA ×4

Waters ×145

* Residue conservation analysis

PDB id:

3gcd

Name:

Toxin/inhibitor

Title:

Structure of the v. Cholerae rtx cysteine protease domain in complex with an aza-leucine peptide inhibitor

Structure:

Rtx toxin rtxa. Chain: a, b, c, d. Fragment: residues 3442-3650. Engineered: yes

Source:

Vibrio cholerae. Organism_taxid: 666. Strain: v. Cholerae 01 biovar eltor str. N16961. Gene: rtxa, vc1451, vc_1451. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.35Å R-factor: 0.221 R-free: 0.265

Authors:

P.J.Lupardus,K.C.Garcia,A.Shen,M.Bogyo

Key ref:

A.Shen et al. (2009). Mechanistic and structural insights into the proteolytic activation of Vibrio cholerae MARTX toxin. Nat Chem Biol, 5, 469-478. PubMed id: 19465933 DOI: 10.1038/nchembio.178

Date:

21-Feb-09 Release date: 26-May-09

Protein chains

Q9KS12  (MARTX_VIBCH) -  Multifunctional-autoprocessing repeats-in-toxin from Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)

Seq: 4558 a.a.

Struc: 202 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.3.1.- - ?????
• Enzyme class 3: E.C.3.4.22.- - ?????
• Enzyme class 4: E.C.6.3.2.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1038/nchembio.178

Nat Chem Biol 5:469-478 (2009)

PubMed id: 19465933

Mechanistic and structural insights into the proteolytic activation of Vibrio cholerae MARTX toxin.

A.Shen, P.J.Lupardus, V.E.Albrow, A.Guzzetta, J.C.Powers, K.C.Garcia, M.Bogyo.

ABSTRACT

MARTX toxins modulate the virulence of a number of Gram-negative Vibrio species. This family of toxins is defined by the presence of a cysteine protease domain (CPD), which proteolytically activates the Vibrio cholerae MARTX toxin. Although recent structural studies of the CPD have uncovered a new allosteric activation mechanism, the mechanism of CPD substrate recognition or toxin processing is unknown. Here we show that interdomain cleavage of MARTX(Vc) enhances effector domain function. We also identify the first small-molecule inhibitors of this protease domain and present the 2.35-A structure of the CPD bound to one of these inhibitors. This structure, coupled with biochemical and mutational studies of the toxin, reveals the molecular basis of CPD substrate specificity and underscores the evolutionary relationship between the CPD and the clan CD caspase proteases. These studies are likely to prove valuable for devising new antitoxin strategies for a number of bacterial pathogens.

Selected figure(s)

Figure 1.
(a) General structures of the main classes of covalent cysteine protease inhibitors in the library used for screening. (b) Sample gel from CPD autoprocessing inhibitor screen.

Figure 2.
(a) Surface topology of the CPD active site. Hydrophobic residues in the substrate binding cleft are highlighted in orange. The aza-peptide epoxide inhibitor (JCP598) is shown as a stick model bound in the substrate binding pocket. The N terminus is shown as a gray ribbon, terminating at Ile5 and highlighting the threading of this region along the surface of the core domain. (b) Close-up 'top' and 'bottom' views of the S1 pocket. Hydrophobic residues in the S1 pocket are shown as orange sticks, and the side chain atoms of the P1 aza-leucine residue are shown as transparent spheres. Hydrogen bonds between the inhibitor backbone and the protein are shown as dashed lines. (c) Superposition of the D and E -strands of caspase-3–aza-Asp epoxide (PDB ID 2C1E) and CPD–aza-leucine epoxide inhibitor structures shown as a cut-away view of the thioether inhibitor adduct bound in the S1 pocket. Caspase-3 is colored purple, and the aza-Asp inhibitor is colored pink. The MARTX[Vc] CPD is colored gray, and the aza-leucine inhibitor is colored yellow.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: Nat Chem Biol (2009, 5, 469-478) copyright 2009.

Figures were selected by an automated process.