title: Conserved water molecules in the specificity pocket of serine proteases and the molecular mechanism of Na+ binding.
abstract: Conservation of clusters of buried water molecules is a structural motif present throughout the serine protease family. Frequently, these clusters are shaped as water channels forming extensive hydrogen-bonding networks linked to the protein backbone. The most conspicuous example is the water channel present in the specificity pocket of trypsin and thrombin. In thrombin, other vitamin K-dependent proteases, and some complement factors, Na+ binds in this water channel and enhances allosterically the catalytic activity of the enzyme, whereas digestive and fibrinolytic proteases are devoid of such regulation. A comparative analysis of proteases with and without Na+ binding capability reveals the role of the water channel in maintaining the structural organization of the specificity pocket and in Na+ coordination. This enables the formulation of a molecular mechanism for Na+ binding in thrombin and leads to the identification of the structural changes necessary to engineer a functional Na+ site and enhanced catalytic activity in trypsin and other proteases.
authors.affiliation: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.
authors.forename: M M
authors.initials: MM
authors.lastname: Krem
authors.forename: E
authors.initials: E
authors.lastname: Di Cera
mesh_terms: D000494:Allosteric Regulation; D000818:Animals; D006801:Humans; D011485:Protein Binding; D051381:Rats; D012697:Serine Endopeptidases / Q000737:chemistry* / Q000378:metabolism; D012964:Sodium / Q000737:chemistry* / Q000378:metabolism; D013917:Thrombin / Q000737:chemistry / Q000378:metabolism; D014867:Water / Q000737:chemistry*
chemical_list: D014867:Water; D012964:Sodium; D012697:Serine Endopeptidases; D013917:Thrombin