Conserved water-mediated H-bonding dynamics of catalytic Asn 175 in plant thiol protease.
The role of invariant water molecules in the activity of plant cysteine protease is ubiquitous in nature. On analysing the 11 different Protein DataBank (PDB) structures of plant thiol proteases, the two invariant water molecules W1 and W2 (W220 and W222 in the template 1PPN structure) were observed to form H-bonds with the O b atom of Asn 175. Extensive energy minimization and molecular dynamics simulation studies up to 2 ns on all the PDB and solvated structures clearly revealed the involvement of the H-bonding association of the two water molecules in fixing the orientation of the asparagine residue of the catalytic triad. From this study,it is suggested that H-bonding of the water molecule at the W1 invariant site better stabilizes the Asn residue at the active site of the catalytic triad.
Nandi
Tapas K
TK
Department of Chemistry, National Institute of Technology, Durgapur 713 209, India.
Bairagya
Hridoy R
HR
Mukhopadhyay
Bishnu P
BP
Sekar
K
K
Sukul
Dipankar
D
Bera
Asim K
AK
D001216:Asparagine / Q000737:chemistry*; D002384:Catalysis; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003546:Cysteine Endopeptidases / Q000737:chemistry*; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D010100:Oxygen / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry*; D010944:Plants / Q000201:enzymology; D017434:Protein Structure, Tertiary; D014867:Water / Q000737:chemistry*
D010940:Plant Proteins; D014867:Water; D001216:Asparagine; D003546:Cysteine Endopeptidases; D010100:Oxygen