1SU1

Structural and biochemical characterization of Yfce, a phosphoesterase from E. coli

Summary for 1SU1

• Entry DOI: 10.2210/pdb1su1/pdb
• Descriptor: Hypothetical protein yfcE, ZINC ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: yfce, structural genomics, phosphoesterase, psi, protein structure initiative, midwest center for structural genomics, mcsg, unknown function
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 92755.63

Authors

Miller, D.J.,Shuvalova, L.,Evdokimova, E.,Savchenko, A.,Yakunin, A.,Anderson, W.F.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2004-03-25, release date: 2004-08-17, Last modification date: 2024-02-14)

Primary citation

Miller, D.J.,Shuvalova, L.,Evdokimova, E.,Savchenko, A.,Yakunin, A.F.,Anderson, W.F.
Structural and biochemical characterization of a novel Mn2+-dependent phosphodiesterase encoded by the yfcE gene.
Protein Sci., 16:1338-1348, 2007

PubMed Abstract: 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.

PubMed: 17586769
DOI: 10.1110/ps.072764907

Experimental method

X-RAY DIFFRACTION (2.25 Å)