Function inferences from a molecular structural model of bacterial ParE toxin

Abstract

Toxin-antitoxin (TA) systems contribute to plasmid stability by a mechanism that relies on the differential stabilities of the toxin and antitoxin proteins and leads to the killing of daughter bacteria that did not receive a plasmid copy at the cell division. ParE is the toxic component of a TA system that constitutes along with RelE an important class of bacterial toxin called RelE/ParE superfamily. For ParE toxin, no crystallographic structure is available so far and rare in vitro studies demonstrated that the target of toxin activity is E. coli DNA gyrase. Here, a 3D Model for E. coli ParE toxin by molecular homology modeling was built using MODELLER, a program for comparative modeling. The Model was energy minimized by CHARMM and validated using PROCHECK and VERIFY3D programs. Resulting Ramachandran plot analysis it was found that the portion residues failing into the most favored and allowed regions was 96.8%. Structural similarity search employing DALI server showed as the best matches RelE and YoeB families. The Model also showed similarities with other microbial ribonucleases but in a small score. A possible homologous deep cleft active site was identified in the Model using CASTp program. Additional studies to investigate the nuclease activity in members of ParE family as well as to confirm the inhibitory replication activity are needed. The predicted Model allows initial inferences about the unexplored 3D structure of the ParE toxin and may be further used in rational design of molecules for structure-function studies.

Keywords: Homology modeling; ParE toxin; RelE/ParE superfamily; TA systems.

Figure 1

(A) Predicted 3-D structure of E. coli ParE toxin. The 3-D model was built from the primary structure of the E. coli ParE toxin (105 amino acids) by adopting an approach to comparative modeling by satisfaction of spatial restraints using MODELLER9v7 program and atomic coordinates of the E. coli RelE toxin as template. (B): Validation of the Model using Ramachandram plot. Ramachandram plot analysis was used to validate the predicted Model. The plot statistics are: 77 (81.9%) residues in most favored regions; 14 (14.9%) residues in additional allowed regions; 2 (2.1%) residues in generously allowed regions; 1 (1.1%) residue in disallowed regions.

Figure 2

Identified active site of the E. coli ParE toxin. A possible deep cleft active site was identified using CASTp program (a) Loop connecting α2 and β2; (b) C-terminal α-helix (α3).