1KDN

STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE

Summary for 1KDN

• Entry DOI: 10.2210/pdb1kdn/pdb
• Descriptor: NUCLEOSIDE DIPHOSPHATE KINASE, MAGNESIUM ION, ALUMINUM FLUORIDE, ... (5 entities in total)
• Functional Keywords: transferase, kinase, atp-binding, phosphotransferase
• Biological source: Dictyostelium discoideum
• Cellular location: Cytoplasm: P22887
• Total number of polymer chains: 3
• Total formula weight: 52055.46

Authors

Cherfils, J.,Xu, Y.W.,Morera, S.,Janin, J. (deposition date: 1996-09-10, release date: 1997-04-21, Last modification date: 2024-02-07)

Primary citation

Xu, Y.W.,Morera, S.,Janin, J.,Cherfils, J.
AlF3 mimics the transition state of protein phosphorylation in the crystal structure of nucleoside diphosphate kinase and MgADP.
Proc.Natl.Acad.Sci.USA, 94:3579-3583, 1997

PubMed Abstract: Nucleoside diphosphate kinase reversibly transfers the gamma-phosphate of ATP onto its active site histidine. We have investigated the transition state of histidine phosphorylation with the high-resolution crystal structures of the enzyme from Dictyostelium discoideum with MgADP and either aluminium or beryllium fluoride. The bound aluminium fluoride species is the neutral species AlF3 and not the more common AlF4-. AlF3 forms a trigonal bipyramid that makes it an accurate analog of the transition state of the gamma-phosphate of ATP undergoing transfer to the catalytic histidine. Its axial ligands are a histidine nitrogen and a beta-phosphate oxygen. Beryllium fluoride also binds at the same position and with the same ligands but in a tetrahedral geometry resembling the Michaelis complex rather than the transition state. The two x-ray structures show explicit enzyme-substrate interactions that discriminate between the ground and the transition states of the reaction. They also illustrate the partially dissociative geometry of the transition state of phosphoryl transfer and demonstrate the potential applications of metallofluorides for the study of kinase mechanisms.

PubMed: 9108019
DOI: 10.1073/pnas.94.8.3579

Experimental method

X-RAY DIFFRACTION (2 Å)