Mechanism of hydrolysis of phosphate esters by the dimetal center of 5'-nucleotidase based on crystal structures.
5'-Nucleotidase belongs to a large superfamily of distantly related dinuclear metallophosphatases including the Ser/Thr protein phosphatases and purple acid phosphatases. The protein undergoes a 96 degrees domain rotation between an open (inactive) and a closed (active) enzyme form. Complex structures of the closed form with the products adenosine and phosphate, and with the substrate analogue inhibitor alpha,beta-methylene ADP, have been determined at 2.1 A and 1.85 A resolution, respectively. In addition, a complex of the open form of 5'-nucleotidase with ATP was analyzed at a resolution of 1.7 A. These structures show that the adenosine group binds to a specific binding pocket of the C-terminal domain. The adenine ring is stacked between Phe429 and Phe498. The N-terminal domain provides the ligands to the dimetal cluster and the conserved His117, which together form the catalytic core structure. However, the three C-terminal arginine residues 375, 379 and 410, which are involved in substrate binding, may also play a role in transition-state stabilization. The beta-phosphate group of the inhibitor is terminally coordinated to the site 2 metal ion. The site 1 metal ion coordinates a water molecule which is in an ideal position for a nucleophilic attack on the phosphorus atom, assuming an in-line mechanism of phosphoryl transfer. Another water molecule bridges the two metal ions.
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Institut für Chemie, Abteilung Kristallographie, Freie Universität Berlin, Germany.
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D015720:5'-Nucleotidase / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism*; D000135:Acid Phosphatase / Q000737:chemistry; D000244:Adenosine Diphosphate / Q000031:analogs & derivatives* / Q000378:metabolism; D000255:Adenosine Triphosphate / Q000378:metabolism; D000818:Animals; D001665:Binding Sites; D002384:Catalysis; D017124:Conserved Sequence; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology*; D006023:Glycoproteins / Q000737:chemistry; D006868:Hydrolysis; D007477:Ions; D008024:Ligands; D008670:Metals / Q000378:metabolism; D008958:Models, Molecular; D010710:Phosphates / Q000378:metabolism*; D010749:Phosphoprotein Phosphatases / Q000737:chemistry; D011485:Protein Binding; D011487:Protein Conformation; D012399:Rotation; D055672:Static Electricity; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D013696:Temperature; D014867:Water / Q000737:chemistry / Q000378:metabolism
D006023:Glycoproteins; D007477:Ions; D008024:Ligands; D008670:Metals; D010710:Phosphates; D014867:Water; C523965:alpha,beta-methyleneadenosine 5'-diphosphate; D000244:Adenosine Diphosphate; D000255:Adenosine Triphosphate; C091137:purple acid phosphatase; D010749:Phosphoprotein Phosphatases; D000135:Acid Phosphatase; D015720:5'-Nucleotidase