Three-dimensional structure of nucleoside diphosphate kinase

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• Nucleoside diphosphate (NDP) kinases are essential enzymes found across all domains of life, catalyzing crucial phosphate transfer reactions.
• X-ray crystallography has revealed conserved structural features of NDP kinases, including a common alphabeta sandwich or ferredoxin fold in subunits of approximately 150 residues.

Purpose of the Study:

• To elucidate the conserved and unique structural elements of NDP kinases.
• To understand the structural basis for the differences in quaternary structure (tetramers vs. hexamers) between bacterial and eukaryotic NDP kinases.
• To provide a structural foundation for understanding the catalytic mechanism of phosphate transfer.

Main Methods:

• X-ray crystallography was employed to determine the three-dimensional structures of NDP kinases.
• Structural analysis of native and phosphorylated enzymes, as well as complexes with substrates, inhibitors, and transition state analogs.

Main Results:

• NDP kinases exhibit a conserved alphabeta sandwich fold, augmented by unique features like an alpha-helix hairpin and Kpn loop forming the nucleotide binding site.
• While eukaryotic NDP kinases are typically hexamers and bacterial ones tetramers, both assemble from identical dimers, with conserved active site environments.
• Structural data support a catalytic mechanism involving the 3'-OH of the sugar and Mg2+ as key contributors to phosphate transfer.

Conclusions:

• The conserved fold and unique nucleotide binding site are central to NDP kinase function across diverse organisms.
• Structural variations, particularly involving C-terminal residues, account for the assembly of hexameric versus tetrameric NDP kinases.
• While the catalytic mechanism is well-supported by structural data, further research is needed to understand NDP kinase roles in DNA binding and other functions.