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Protein Science (2007), 16:1338-1348. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Structural and biochemical characterization of a novel Mn2+-dependent phosphodiesterase encoded by the yfcE gene

Darcie J. Miller1,2, Ludmilla Shuvalova1, Elena Evdokimova3, Alexei Savchenko3, Alexander F. Yakunin3, and Wayne F. Anderson1,2

1 Department of Molecular Pharmacology and Biological Chemistry, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, USA
2 Drug Discovery Program, Northwestern University, Feinberg School of Medicine, Chicago, Illinois 60611, USA
3 C. H. Best Institute, University of Toronto, Toronto, Ontario M5G 1L6, Canada

(RECEIVED January 15, 2007; FINAL REVISION April 1, 2007; ACCEPTED April 3, 2007)

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 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.

Keywords: enzymes; metalloproteins; crystallography; genomics-structural; phosphodiesterase


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Nucleic Acids Res., December 3, 2007; 35(22): 7721 - 7732.
[Abstract] [Full Text] [PDF]


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