Title

Function inferences from a molecular structural model of bacterial ParE toxin

Authors

Luiz Carlos Bertucci Barbosa, Saulo Santesso Garrido, Anderson Garcia, Davi Barbosa Delfino, Reinaldo Marchetto^*

Affiliation

Institute of Chemistry, UNESP – Univ Estadual Paulista, Department of Biochemistry and Technological Chemistry, Araraquara, São Paulo, Brazil.

Email

marcheto@iq.unesp.br

Article Type

Hypothesis

Date

Received March 08, 2010; accepted April 09, 2010; published April 30, 2010

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

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

Citation

Barbosa et al. Bioinformation 4(10): 000-000 (2010)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.