Function Inferences from a Molecular Structural Model of YoeBXn Toxin from Xenorhabdus n emat ophila

To xin-antitoxin (TA) co mplexes function in programmed cell death or stress response mechanisms in bacteria. The YefM-YoeB TA co mplex of Escherichia coli consists of YoeB to xin that is counteracted by YefM antito xin. When liberated fro m the co mplex, YoeB acts as an endoribonuclease, preferentially cleaving 3' of purine nucleotides. In this study YoeBXn to xin fro m Xenorhabdus nematophila is reported for first time. As no crystallographic structure is available so far, therefore a 3-D Model for Xenorhabdus nematophila YoeBXn to xin was built using SWISS-MODEL, a program for automated modeling. The Model was further validated using VERIFY-3D program as well as Ramachandran plot analysis program. Ramachandran plot analysis showed that 97.56% residues fall in the most favoured and allowed regions. Structural similarity search employing PHYRE server showed as the best matches YoeB and RelE families. The Model also showed similarities with other microbial ribonucleases. A possible homologous deep cleft of active site was identified by CASTp programme and Model was v iewed by CHIM ERA software. Additional studies to investigate the endoribonuclease activity in YoeBXn to xin p rotein are needed. The predicted Model allows in itial inferences about the unexplored 3-D structure of the YoeBXn to xin and may be further used in rational design of molecules for structure-function studies.