Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium.
Nucleoside diphosphate kinase (NDP kinase) has a ping-pong mechanism with a phosphohistidine intermediate. Crystals of the enzymes from Dictyostelium discoideum and from Drosophila melanogaster were treated with phosphoramidate, and their X-ray structures were determined at 2.1 and 2.2 A resolution, respectively. The atomic models, refined to R factors below 20%, show no conformation change relative to the free proteins. In both enzymes, the active site histidine was phosphorylated on N delta, and it was the only site of phosphorylation. The phosphate group interacts with the hydroxyl group of Tyr56 and with protein-bound water molecules. Its environment is compared with that of phosphohistidines in succinyl-CoA synthetase and in phosphocarrier proteins. The X-ray structures of phosphorylated NDP kinase and of previously determined complexes with nucleoside diphosphates provide a basis for modeling the Michaelis complex with a nucleoside triphosphate, that of the phosphorylated protein with a nucleoside diphosphate, and the transition state of the phosphate transfer reaction in which the gamma-phosphate is pentacoordinated.
Moréra
S
S
Laboratoire de Biologie Structurale, UMR 9920 CNRS-Université Paris-Sud, Gif-sur-Yvette, France.
Chiadmi
M
M
LeBras
G
G
Lascu
I
I
Janin
J
J
D000818:Animals; D001665:Binding Sites; D002384:Catalysis; D018360:Crystallography, X-Ray; D004023:Dictyostelium / Q000201:enzymology / Q000235:genetics; D004331:Drosophila melanogaster / Q000201:enzymology / Q000235:genetics; D004563:Electrochemistry; D004926:Escherichia coli / Q000235:genetics; D006639:Histidine / Q000031:analogs & derivatives / Q000378:metabolism; D008958:Models, Molecular; D015394:Molecular Structure; D009701:Nucleoside-Diphosphate Kinase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D010710:Phosphates / Q000378:metabolism*; D010766:Phosphorylation; D011487:Protein Conformation; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
D010710:Phosphates; D011994:Recombinant Proteins; D006639:Histidine; D009701:Nucleoside-Diphosphate Kinase; C005436:phosphohistidine