title: A structure-based proposal for the catalytic mechanism of the bacterial acid phosphatase AphA belonging to the DDDD superfamily of phosphohydrolases.
abstract: The Escherichia coli gene aphA codes for a periplasmic acid phosphatase called AphA, belonging to class B bacterial phosphatases, which is part of the DDDD superfamily of phosphohydrolases. After our first report about its crystal structure, we have started a series of crystallographic studies aimed at understanding of the catalytic mechanism of the enzyme. Here, we report three crystal structures of the AphA enzyme in complex with the hydrolysis products of nucleoside monophosphate substrates and a fourth with a proposed intermediate analogue that appears to be covalently bound to the enzyme. Comparison with the native enzyme structure and with the available X-ray structures of different phosphatases provides clues about the enzyme chemistry and allows us to propose a catalytic mechanism for AphA, and to discuss it with respect to the mechanism of other bacterial and human phosphatases.
authors.affiliation: Dipartimento di Chimica, Università di Siena, Via Aldo Moro, I-53100 Siena, Italy.
authors.forename: Vito
authors.initials: V
authors.lastname: Calderone
authors.forename: Costantino
authors.initials: C
authors.lastname: Forleo
authors.forename: Manuela
authors.initials: M
authors.lastname: Benvenuti
authors.forename: Maria Cristina
authors.initials: MC
authors.lastname: Thaller
authors.forename: Gian Maria
authors.initials: GM
authors.lastname: Rossolini
authors.forename: Stefano
authors.initials: S
authors.lastname: Mangani
mesh_terms: D000135:Acid Phosphatase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D000249:Adenosine Monophosphate / Q000737:chemistry / Q000378:metabolism; D000595:Amino Acid Sequence; D001665:Binding Sites; D002384:Catalysis; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D003843:Deoxycytidine Monophosphate / Q000737:chemistry / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010744:Phosphoric Monoester Hydrolases / Q000737:chemistry* / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D020836:Protein Structure, Quaternary; D021122:Protein Subunits / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: D029968:Escherichia coli Proteins; D008024:Ligands; D021122:Protein Subunits; D003843:Deoxycytidine Monophosphate; D000249:Adenosine Monophosphate; D000135:Acid Phosphatase; C508128:AphA protein, E coli; D010744:Phosphoric Monoester Hydrolases