1BUX

3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

Summary for 1BUX

• Entry DOI: 10.2210/pdb1bux/pdb
• Descriptor: NUCLEOSIDE DIPHOSPHATE KINASE, 3'-PHOSPHATE-ADENOSINE-5'-PHOSPHATE SULFATE (2 entities in total)
• Functional Keywords: phosphotransferase, inhibitor, paps
• Biological source: Dictyostelium discoideum
• Cellular location: Cytoplasm: P22887
• Total number of polymer chains: 3
• Total formula weight: 51970.80

Authors

Xu, Y.,Schneider, B.,Deville-Bonne, D.,Veron, M.,Janin, J. (deposition date: 1998-09-07, release date: 1999-04-27, Last modification date: 2024-02-07)

Primary citation

Schneider, B.,Xu, Y.W.,Janin, J.,Veron, M.,Deville-Bonne, D.
3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity.
J.Biol.Chem., 273:28773-28778, 1998

PubMed Abstract: Nucleoside diphosphate (NDP) kinase catalyzes the phosphorylation of ribo- and deoxyribonucleosides diphosphates into triphosphates. NDP kinase is also involved in malignant tumors and was shown to activate in vitro transcription of the c-myc oncogene by binding to its NHE sequence. The structure of the complex of NDP kinase with bound ADP shows that the nucleotide adopts a different conformation from that observed in other phosphokinases with an internal H bond between the 3'-OH and the beta-O made free by the phosphate transfer. We use intrinsic protein fluorescence to investigate the inhibitory and binding potential of nucleotide analogues phosphorylated in 3'-OH position of the ribose to both wild type and F64W mutant NDP kinase from Dictyostelium discoideum. Due to their 3'-phosphate, 5'-phosphoadenosine 3'-phosphate (PAP) and adenosine 3'-phosphate 5'-phosphosulfate (PAPS) can be regarded as structural analogues of enzyme-bound ADP. The KD of PAPS (10 microM) is three times lower than the KD of ADP. PAPS also acts as a competitive inhibitor toward natural substrates during catalysis, with a KI in agreement with binding data. The crystal structure of the binary complex between Dictyostelium NDP kinase and PAPS was solved at 2.8-A resolution. It shows a new mode of nucleotide binding at the active site with the 3'-phosphate of PAPS located near the catalytic histidine, at the same position as the gamma-phosphate in the transition state. The sulfate group is directed toward the protein surface. PAPS will be useful for the design of high affinity drugs targeted to NDP kinases.

PubMed: 9786875
DOI: 10.1074/jbc.273.44.28773

Experimental method

X-RAY DIFFRACTION (2.8 Å)