Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site

• Published in: Journal of structural biology Vol. 189; no. 2; pp. 81 - 86
• Main Authors: Gajadeera, Chathurada S., Zhang, Xinyi, Wei, Yinan, Tsodikov, Oleg V.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.02.2015
• Subjects: Bacterial Proteins - chemistry; Catalytic Domain; Crystallography, X-Ray; Enzyme; Hydrogen Bonding; Hydrolase; Inorganic Pyrophosphatase - chemistry; Kinetics; Manganese - chemistry; Models, Molecular; Novel drug target; Phosphatase; Phosphate metabolism; Phosphates - chemistry; Protein Binding; Protein Structure, Quaternary; Pyrophosphorolysis; Staphylococcus aureus - enzymology; Novel drug target; PNP; Pyrophosphorolysis; Hydrolase; Enzyme; PPiase; Phosphate metabolism; Phosphatase; SA
• ISSN: 1047-8477; 1095-8657
• DOI: 10.1016/j.jsb.2014.12.003

Cytoplasmic inorganic pyrophosphatase (PPiase) is an enzyme essential for survival of organisms, from bacteria to human. PPiases are divided into two structurally distinct families: family I PPiases are Mg2+-dependent and present in most archaea, eukaryotes and prokaryotes, whereas the relatively less understood family II PPiases are Mn2+-dependent and present only in some archaea, bacteria and primitive eukaryotes. Staphylococcus aureus (SA), a dangerous pathogen and a frequent cause of hospital infections, contains a family II PPiase (PpaC), which is an attractive potential target for development of novel antibacterial agents. We determined a crystal structure of SA PpaC in complex with catalytic Mn2+ at 2.1Å resolution. The active site contains two catalytic Mn2+ binding sites, each half-occupied, reconciling the previously observed 1:1 Mn2+:enzyme stoichiometry with the presence of two divalent metal ion sites in the apo-enzyme. Unexpectedly, despite the absence of the substrate or products in the active site, the two domains of SA PpaC form a closed active site, a conformation observed in structures of other family II PPiases only in complex with substrate or product mimics. A region spanning residues 295–298, which contains a conserved substrate binding RKK motif, is flipped out of the active site, an unprecedented conformation for a PPiase. Because the mutant of Arg295 to an alanine is devoid of activity, this loop likely undergoes an induced-fit conformational change upon substrate binding and product dissociation. This closed conformation of SA PPiase may serve as an attractive target for rational design of inhibitors of this enzyme.