title: Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis.
abstract: Family I inorganic pyrophosphatases (PPiases) are ubiquitous enzymes that are critical for phosphate metabolism in all domains of life. The detailed catalytic mechanism of these enzymes, including the identity of the general base, is not fully understood. We determined a series of crystal structures of the PPiase from Mycobacterium tuberculosis (Mtb PPiase) bound to catalytic metals, inorganic pyrophosphate (PPi; the reaction substrate) and to one or two inorganic phosphate ions (Pi; the reaction product), ranging in resolution from 1.85 to 3.30Å. These structures represent a set of major kinetic intermediates in the catalytic turnover pathway for this enzyme and suggest an order of association and dissociation of the divalent metals, the substrate and the two products during the catalytic turnover. The active site of Mtb PPiase exhibits significant structural differences from the well characterized Escherichia coli PPiase in the vicinity of the bound PPi substrate. Prompted by these differences, quantum mechanics/molecular mechanics (QM/MM) analysis yielded an atomic description of the hydrolysis step for Mtb PPiase and, unexpectedly, indicated that Asp89, rather than Asp54 that was proposed for E. coli PPiase, can abstract a proton from a water molecule to activate it for a nucleophilic attack on the PPi substrate. Mutagenesis studies of the key Asp residues of Mtb PPiase supported this mechanism. This combination of structural and computational analyses clarifies our understanding of the mechanism of family I PPiases and has potential utility for rational development of drugs targeting this enzyme.
authors: Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA.
authors: Andrew C
authors: AC
authors: Pratt
authors: Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.
authors: Sajeewa W
authors: SW
authors: Dewage
authors: Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA.
authors: Allan H
authors: AH
authors: Pang
authors: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.
authors: Tapan
authors: T
authors: Biswas
authors: Food and Drug Administration, Center for Drug Evaluation and Research, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA.
authors: Sandra
authors: S
authors: Barnard-Britson
authors: Department of Chemistry, Wayne State University, Detroit, MI 48202, USA. Electronic address: andres@chem.wayne.edu.
authors: G Andrés
authors: GA
authors: Cisneros
authors: Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA. Electronic address: oleg.tsodikov@uky.edu.
authors: Oleg V
authors: OV
authors: Tsodikov
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D055162:Biocatalysis; D002118:Calcium / Q000737:chemistry; D020134:Catalytic Domain; D011756:Diphosphates / Q000737:chemistry; D004926:Escherichia coli / Q000201:enzymology; D006860:Hydrogen Bonding; D006868:Hydrolysis; D043564:Inorganic Pyrophosphatase / Q000737:chemistry*; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009169:Mycobacterium tuberculosis / Q000201:enzymology*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D040681:Structural Homology, Protein
chemical_list: D001426:Bacterial Proteins; D011756:Diphosphates; C107241:diphosphoric acid; D043564:Inorganic Pyrophosphatase; D002118:Calcium
keywords: Crystallography; Enzyme catalysis; Molecular dynamics; Phosphatase; Structure-function