2BEF: Crystal Structure Of Ndp Kinase Complexed With Mg, Adp, And Bef3

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.
PDB ID: 2BEFDownload
MMDB ID: 8381
PDB Deposition Date: 1998/5/26
Updated in MMDB: 2012/12
Experimental Method:
x-ray diffraction
Resolution: 2.3  Å
Source Organism:
Similar Structures:
Biological Unit for 2BEF: hexameric; determined by author and by software (PISA,PQS)
Molecular Components in 2BEF
Label Count Molecule
Proteins (6 molecules)
Nucleoside Diphosphate Kinase(Gene symbol: ndkC-1)
Molecule annotation
Chemicals (12 molecules)
* Click molecule labels to explore molecular sequence information.

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