Structural insight
into PNAG binding and partial De-N-acetylation modification site of IcaB protein
in Staphylococcus epidermidis
Ramachandira Prabu, Mohanty Amaresh Kumar, Raziya Shaik, Sarada R. and Veeramani
T.
Res. J. Biotech.; Vol. 20(11); 21-29;
doi: https://doi.org/10.25303/2011rjbt021029; (2025)
Abstract
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.
