1NDP

ADENOSINE 5'-DIPHOSPHATE BINDING AND THE ACTIVE SITE OF NUCLEOSIDE DIPHOSPHATE KINASE

Summary for 1NDP

• Entry DOI: 10.2210/pdb1ndp/pdb
• Descriptor: NUCLEOSIDE DIPHOSPHATE KINASE, ADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: phosphotransferase
• Biological source: Dictyostelium discoideum
• Cellular location: Cytoplasm: P22887
• Total number of polymer chains: 2
• Total formula weight: 34511.38

Authors

Janin, J.,Morera, S.,Dumas, C.,Lascu, I.,Lebras, G.,Veron, M. (deposition date: 1993-11-29, release date: 1994-04-30, Last modification date: 2024-02-14)

Primary citation

Morera, S.,Lascu, I.,Dumas, C.,LeBras, G.,Briozzo, P.,Veron, M.,Janin, J.
Adenosine 5'-diphosphate binding and the active site of nucleoside diphosphate kinase.
Biochemistry, 33:459-467, 1994

PubMed Abstract: 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 alpha- to the beta-phosphate which approaches the imidazole group of His 122 from the N delta side. The geometry at the active site in the ADP-Mg2+ complex suggests a mechanism for catalysis whereby the gamma-phosphate of a nucleoside triphosphate can be transferred onto His 122 with a minimum of atomic motion.

PubMed: 8286376
DOI: 10.1021/bi00168a010

Experimental method

X-RAY DIFFRACTION (2.2 Å)