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

Chathurada S. Gajadeera, Xinyi Zhang, Yinan Wei, Oleg V. Tsodikov

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)81-86
Number of pages6
JournalJournal of Structural Biology
Issue number2
StatePublished - Feb 1 2015
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by the Igniting Research Collaboration Award from the University of Kentucky (to O.V.T. and Y.W.) and Kentucky Science & Engineer Foundation ( KSEF-148-502-14-332 ; to Y.W.). We thank Sandra Barnard-Britson for preliminary purification and crystallization of SA PPiase and Zdzislaw Wawrzak and the staff of sector LS-CAT at the Advanced Photon Source, Argonne National Laboratory, for the assistance with the synchrotron data collection.

Publisher Copyright:
© 2014 Elsevier Inc.


  • Enzyme
  • Hydrolase
  • Novel drug target
  • Phosphatase
  • Phosphate metabolism
  • Pyrophosphorolysis


Dive into the research topics of 'Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site'. Together they form a unique fingerprint.

Cite this