|
KMID : 1132720230210010007
|
|
Genomics & Informatics
2023 Volume.21 No. 1 p.7 ~ p.7
|
|
|
In silico annotation of a hypothetical protein from Listeria monocytogenes EGD-e unfolds a toxin protein of the type II secretion system
|
|
Maisha Tasneem
Jessica Ang
Lishan Yang
Kazi Modasser Hossain
Tasnim Binta Osman
Fazley Rabbi
|
|
|
Abstract
|
|
|
|
The gram-positive bacterium Listeria monocytogenes is an important foodborne intracellular pathogen that is widespread in the environment. The functions of hypothetical proteins (HP) from various pathogenic bacteria have been successfully annotated using a variety of bioinformatics strategies. In this study, a HP Imo0888 (NP_464414.1) from the Listeria monocytogenes EGD-e strain was annotated using several bioinformatics tools. Various techniques, including CELLO, PSORTb, and SOSUIGramN, identified the candidate protein as cytoplasmic. Domain and motif analysis revealed that the target protein is a PemK/MazF-like toxin protein of the type II toxin-antitoxin system (TAS) which was consistent with BLASTp analysis. Through secondary structure analysis, we found the random coil to be the most frequent. The Alpha Fold 2 Protein Structure Prediction Database was used to determine the three-dimensional (3D) structure of the HP using the template structure of a type II TAS PemK/MazF family toxin protein (DB ID_AFDB: A0A4B9HQB9) with 99.1% sequence identity. Various quality evaluation tools, such as PROCHECK, ERRAT, Verify 3D, and QMEAN were used to validate the 3D structure. Following the YASARA energy minimization method, the target protein's 3D structure became more stable. The active site of the developed 3D structure was determined by the CASTp server. Most pathogens that harbor TAS create a crucial risk to human health. Our aim to annotate the HP Imo088 found in Listeria could offer a chance to understand bacterial pathogenicity and identify a number of potential targets for drug development.
|
|
|
KEYWORD
|
|
|
hypothetical protein, in silico characterization, Listeria monocytogenes, PemK/MazF-like toxin, three-dimensional structure, type II toxin-antitoxin system
|
|
|
FullTexts / Linksout information
|
|
|
|
|
|
Listed journal information
|
|
|
|
|