1HIY

Binding of nucleotides to NDP kinase

Summary for 1HIY

• Entry DOI: 10.2210/pdb1hiy/pdb
• Related: 1B4S 1B99 1BUX 1F3F 1F6T 1HHQ 1KDN 1LEO 1LWX 1NCL 2BEF
• Descriptor: NUCLEOSIDE DIPHOSPHATE KINASE, 3'-DEOXY 3'-AMINO ADENOSINE-5'-DIPHOSPHATE (3 entities in total)
• Functional Keywords: metabolic role, transferase, kinase
• Biological source: DICTYOSTELIUM DISCOIDEUM
• Total number of polymer chains: 3
• Total formula weight: 51727.66

Authors

Cervoni, L.,Lascu, I.,Xu, Y.,Gonin, P.,Morr, M.,Merouani, M.,Janin, J.,Giartoso, A. (deposition date: 2001-01-05, release date: 2001-05-31, Last modification date: 2023-12-13)

Primary citation

Cervoni, L.,Lascu, I.,Xu, Y.,Gonin, P.,Morr, M.,Merouani, M.,Janin, J.,Giartosio, A.
Binding of Nucleotides to Nucleoside Diphosphate Kinase: A Calorimetric Study.
Biochemistry, 40:4583-, 2001

PubMed Abstract: The source of affinity for substrates of human nucleoside diphosphate (NDP) kinases is particularly important in that its knowledge could be used to design more effective antiviral nucleoside drugs (e.g., AZT). We carried out a microcalorimetric study of the binding of enzymes from two organisms to various nucleotides. Isothermal titration calorimetry has been used to characterize the binding in terms of Delta G degrees, Delta H degrees and Delta S degrees. Thermodynamic parameters of the interaction of ADP with the hexameric NDP kinase from Dictyostelium discoideum and with the tetrameric enzyme from Myxococcus xanthus, at 20 degrees C, were similar and, in both cases, binding was enthalpy-driven. The interactions of ADP, 2'deoxyADP, GDP, and IDP with the eukaryotic enzyme differed in enthalpic and entropic terms, whereas the Delta G degrees values obtained were similar due to enthalpy--entropy compensation. The binding of the enzyme to nonphysiological nucleotides, such as AMP--PNP, 3'deoxyADP, and 3'-deoxy-3'-amino-ADP, appears to differ in several respects. Crystallography of the protein bound to 3'-deoxy-3'-amino-ADP showed that the drug was in a distorted position, and was unable to interact correctly with active site side chains. The interaction of pyrimidine nucleoside diphosphates with the hexameric enzyme is characterized by a lower affinity than that with purine nucleotides. Titration showed the stoichiometry of the interaction to be abnormal, with 9--12 binding sites/hexamer. The presence of supplementary binding sites might have physiological implications.

PubMed: 11294625
DOI: 10.1021/BI002432S

Experimental method

X-RAY DIFFRACTION (2.6 Å)