Computer Modeling of the Three-dimensional Structure of the Active Site of Human Prolidase
GUO Chong\|zhi 1) , XUAN Zhen\|yu 2) , CHEN Run\|sheng 2) , SUN Man\|ji 1)* ( 1) Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China; 2) Institute of Biophysics,Chinese Academy of Sciences, Beijing 100101, China)
Prolidase is a wide\|spread intracellular dipeptidase which specifically cleaves the dipeptide bearing a carboxyl terminus of proline or hydroxyproline and only shows enzymatic activity to trans\|peptide bond. Prolidase plays an important role in the proline metabolism, collagen synthesis and cell growth. It was reported recently that prolidase extracted from Alteromonas bacteria could hydrolyze soman, the organophosphorus acid anhydrolase from this bacteria showed prolidase activity, and the recombinant human liver prolidase also shows the activities mentioned above. So it was important from both practical and theoretical point of view to study the active site structure of prolidase. The computer modeling of the three\|dimensional structure of prolidase was carried out by means of threading, since the crystal structure of prolidase has not been reported up to now. The three dimensional structure of C\|terminal domain was modeled with methionine amino\|peptidase (1MAT) from E.coli as template. The active site structure of human prolidase was predicted by profile\|3D evaluation and charge distribution analysis. The active site of the modeled structure of human prolidase locates at the C\|terminal domain, forms a hydrophobic pocket by six ��\|sheets surrounding by five ��\|helixes and some loops outside. The active site sits in the middle of the hydrophobic structure that contains five conserved amino acids to form a relatively strong negative charge region surrounded by three positive charge regions. It was found that Mn 2+ and Co 2+ was critically important to the enzyme activity, but contributed little to the protein structure, suggesting that they might presumably play a role in the charge transfer of the catalytic reaction.