PDBsum entry 1pp0

Toxin

PDB id: 1pp0

Contents

Protein chains

191 a.a. *

Ligands

ACY ×13

Waters ×756

* Residue conservation analysis

PDB id:

1pp0

Name:

Toxin

Title:

Volvatoxin a2 in monoclinic crystal

Structure:

Volvatoxin a2. Chain: a, b, c, d

Source:

Volvariella volvacea. Organism_taxid: 36659

Biol. unit:

Tetramer (from PQS)

Resolution:

1.42Å R-factor: 0.229 R-free: 0.255

Authors:

S.-C.Lin,Y.-C.Lo,J.-Y.Lin,Y.-C.Liaw

Key ref:

S.C.Lin et al. (2004). Crystal structures and electron micrographs of fungal volvatoxin A2. J Mol Biol, 343, 477-491. PubMed id: 15451675 DOI: 10.1016/j.jmb.2004.08.045

Date:

16-Jun-03 Release date: 24-Aug-04

Protein chains

Q6USC4  (Q6USC4_9AGAR) -  Volvatoxin A2 from Volvariella volvacea

Seq: 217 a.a.

Struc: 191 a.a.

DOI no: 10.1016/j.jmb.2004.08.045

J Mol Biol 343:477-491 (2004)

PubMed id: 15451675

Crystal structures and electron micrographs of fungal volvatoxin A2.

S.C.Lin, Y.C.Lo, J.Y.Lin, Y.C.Liaw.

ABSTRACT

Membrane adhesion and insertion of protein are essential to all organisms, but the underlying mechanisms remain largely unknown. Membrane pore-forming toxins (PFTs) are potential model systems for studying these mechanisms. We have determined the crystal structures of volvatoxin A2 (VVA2), a fungal PFT from Volvariella volvacea, using Br-multiple-wavelength anomalous diffraction (MAD). The VVA2 structures obtained at pH 4.6, pH 5.5 and pH 6.5 were refined to resolutions of 1.42 A, 2.6 A and 3.2 A, respectively. The structures reveal that the VVA2 monomer contains a single alpha/beta domain. Most of the VVA2 surface is occupied by its oligomerization motif and two putative heparin-binding motifs. Residues Ala91 to Ala101 display several conformations at different pH values, which might be under the control of His87. We also found that the shape of one putative heparin-binding motif in VVA2 appears similar to those found in fibroblast growth factors, and the other one displays a linear polypeptide. Our results suggest several possible intermediates of protein assembly in solution and protein adhering to cell membranes before conformational changes. The electron micrographs of VVA2 molecules in solution, at a protein concentration of 1 microg ml(-1), show that they can assemble into filament-like or braid-like oligomers in a pH-dependent way. In addition, the arc-shaped VVA2 structure obtained at pH 6.5 suggests that VVA2 could form a two-layered helical oligomer with 18 subunits per turn. The structures presented here could be used to elucidate the pore-formation mechanisms of VVA2 and its structural neighbors, Cyt toxins from Bacillus thuringiensis.

Selected figure(s)

Figure 8.
Figure 8. A helical oligomer model of VVA2 assembly. (a) Molecular organization in VVA2 strip crystals. Five subunits in one asymmetric unit of strip crystals are labeled. The intermolecular interfaces between layer AB and layer CD are marked by the name of secondary elements. (b) The electrostatic potential surface of the opaque pentamer in (c). Anion-binding sites are indicated. (c) Stereo view of an extended arc-shaped oligomer generated by the molecular packing in (a). The opaque pentamer is rotated 90° around the horizontal axis relative to (a). The transparent pentamer indicates the generated model after superimposition. (d) Stereo view of a unique two-layered helical oligomer model. Subunits are colored as in (a). This view of the helical model also shows the 9-fold symmetry. The membrane-embedded regions are colored in light blue.

Figure 9.
Figure 9. Comparison of the structures and the sequences between VVA2 and Cyts. (a) Stereo C^a trace of the superimposed VVA2 and Cyt2Aa1. VVA2 and Cyt2Aa1 are shown in blue and red, respectively. The absolutely conserved residues are shown as ball-and-sticks. (b) Alignment of sequences of VVA2 with Cyt2Aa1 and Cyt1Aa1 from B. thuringiensis. The alignment is according to structural superimposition, as well as sequence identities. Secondary structural elements of VVA2 and Cyt2Aa1 are shown in pink and green, respectively, and 3[10]-helices are indicated. Conservative residues are masked in crimson (absolutely conserved) or yellow. The red residues indicate low-toxicity mutations in Cyt1Aa1.18 The sequences of Cyt toxins after proteolytic activation are shown.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 343, 477-491) copyright 2004.

Figures were selected by the author.