Structural insight into PNAG binding and partial De-N-acetylation modification site of IcaB protein in Staphylococcus epidermidis

De-N-acetylation of Poly-N-acetylglucosamine (dPNAG) is an extracellular exopolysaccharide for biofilm development. Staphylococcus epidermidis, IcaB is poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase belonging to CE4s family of carbohydrate esterase. It overlaps with IcaC gene at 3’-end. IcaB present in periplasmic region of cell membrane required for partial de-N-acetylation of PNAG, yet details of crystal structure are unknown. We have characterized IcaB gene sequence first which may act as promoter for IcaC gene regulation by enhancing or silencing in Staphylococcus epidermidis. Protein threading was used for construction of truncated IcaB three-dimensional structure. Post-translational modification site as acetylation, ubiquitination, phosphorylation except glycosylation was commonly found in IcaB protein sequence. DXD, DXH, NXS, HD, RXXR signature sequences were required for IcaB metal binding and enzyme catalytic activity. Binding free energy was calculated for IcaB-GluNAc ligand docking to form hydrogen bond with critical amino acids showing ΔG score −11.95 KJ/mol using Autodock 4.2.6. Ligand docking and molecular dynamics simulation (MDS) were performed to evaluate the stability of IcaB, IcaB-GlcNAc binding complexes packed within active site amino acids throughout trajectories captured with time scale 100 ns period using GROMACS 4.5. Different binding energies were calculated for IcaB-GlcNAc complex using GROMACS tools MM-PBSA with perceptive to van der Waal energy, electrostatic energy and polar solvation energy, SASA energy.