Structural and Biochemical Characterization of a Novel Mn2+-dependent Phosphodiesterase Encoded by the yfcE Gene

Protein Sci. 2007 Jul;16(7):1338-48. doi: 10.1110/ps.072764907.


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 A resolution. YfcE has a beta-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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Catalysis / drug effects
  • Crystallography, X-Ray
  • Deoxyribonucleases / metabolism
  • Dimerization
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Hydrolysis / drug effects
  • Manganese / chemistry
  • Manganese / metabolism*
  • Models, Molecular
  • Molecular Sequence Data
  • Phosphates / pharmacology
  • Phosphoric Diester Hydrolases / chemistry*
  • Phosphoric Diester Hydrolases / genetics
  • Phosphoric Diester Hydrolases / metabolism
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid
  • Structural Homology, Protein
  • Substrate Specificity
  • Sulfates / pharmacology


  • Escherichia coli Proteins
  • Phosphates
  • Sulfates
  • Manganese
  • Deoxyribonucleases
  • Phosphoric Diester Hydrolases