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Adenosine 5'-diphosphate binding and the active site of nucleoside diphosphate kinase

Adenosine 5'-diphosphate binding and the active site of nucleoside diphosphate kinase

Biochemistry 33(2): 459-467

The X-ray structure of nucleoside diphosphate kinase (NDP kinase) from the slime mold Dictyostelium discoideum has been determined to 2.2-A resolution and refined to an R-factor of 0.19 with and without bound ADP-Mg2+. The nucleotide binds near His 122, a residue which becomes phosphorylated during the catalytic cycle. The mode of binding is different from that observed in other phosphokinases, and it involves no glycine-rich sequence. The adenine base makes only nonpolar contacts with the protein. It points outside, explaining the lack of specificity of NDP kinase toward the base. The ribose 2'- and 3'-hydroxyls and the pyrophosphate moiety are H-bonded to polar side chains. A Mg2+ ion bridges the a- to the b-phosphate which approaches the imidazole group of His 122 from the Nd side. The geometry at the active site in the ADP-Mg2+ complex suggests a mechanism for catalysis whereby the c-phosphate of a nucleoside triphosphate can be transferred onto His 122 with a minimum of atomic motion. Copyright 1994, American Chemical Society. .

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Accession: 008110739

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PMID: 8286376

DOI: 10.1021/bi00168a010

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