1NSP: Mechanism Of Phosphate Transfer By Nucleoside Diphosphate Kinase: X- Ray Structures Of A Phospho-Histidine 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.
PDB ID: 1NSPDownload
MMDB ID: 50520
PDB Deposition Date: 1995/4/18
Updated in MMDB: 2007/10
Experimental Method:
x-ray diffraction
Resolution: 2.1  Å
Source Organism:
Similar Structures:
Biological Unit for 1NSP: hexameric; determined by author and by software (PISA,PQS)
Molecular Components in 1NSP
Label Count Molecule
Proteins (6 molecules)
Nucleoside Diphosphate Kinase(Gene symbol: ndkC-1)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

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