Structural and biochemical characterization of a novel Mn 2+-dependent phosphodiesterase encoded by the yfcE gene

Darcie J. Miller, Ludmilla Shuvalova, Elena Evdokimova, Alexei Savchenko, Alexander F. Yakunin, Wayne F. Anderson*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

23 Scopus citations


Escherichia coli YfcE belongs to a conserved protein family within the calcineurin-like phosphoesterase superfamily (Pfam00149) that is widely distributed in bacteria and archaea. Superfamily members are metallophosphatases that include monoesterases and diesterases involved in a variety of cellular functions. YfcE exhibited catalytic activity against bis-p-nitrophenyl phosphate, a general substrate for phosphodiesterases, and had an absolute requirement for Mn2+. However, no activity was observed with phosphodiesters and over 50 naturally occurring phosphomonoesters. The crystal structure of the YfcE phosphodiesterase has been determined to 2.25 Å resolution. YfcE has a β-sandwich architecture similar to metallophosphatases of common ancestral origin. Unlike its more complex homologs that have added structural elements for regulation and substrate recognition, the relatively small 184-amino-acid protein has retained its ancestral simplicity. The tetrameric protein carries two zinc ions per active site from the E. coli extract that reflect the conserved di-Mn2+ active site geometry. A cocrystallized sulfate inhibitor mimics the binding of phosphate moeities in known ligand/phosphatase complexes. Thus, YfcE has a similar active site and biochemical mechanism as well-characterized superfamily members, while the YfcE phosphodiester-containing substrate is unique. Published by Cold Spring Harbor Laboratory Press.

Original languageEnglish (US)
Pages (from-to)1338-1348
Number of pages11
JournalProtein Science
Issue number7
StatePublished - Jul 2007


  • Crystallography
  • Enzymes
  • Genomics-structural
  • Metalloproteins
  • Phosphodiesterase

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology


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