4C6A

High Resolution Structure of the Nucleoside diphosphate kinase

Summary for 4C6A

• Entry DOI: 10.2210/pdb4c6a/pdb
• Descriptor: NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC, DI(HYDROXYETHYL)ETHER (3 entities in total)
• Functional Keywords: transferase, phosphotransferase
• Biological source: DICTYOSTELIUM DISCOIDEUM
• Cellular location: Cytoplasm: P22887
• Total number of polymer chains: 1
• Total formula weight: 16710.16

Authors

Priet, S.,Ferron, F.,Alvarez, K.,Verron, M.,Canard, B. (deposition date: 2013-09-18, release date: 2013-11-20, Last modification date: 2023-12-20)

Primary citation

Priet, S.,Roux, L.,Saez-Ayala, M.,Ferron, F.,Canard, B.,Alvarez, K.
Enzymatic Synthesis of Acyclic Nucleoside Thiophosphonate Diphosphates: Effect of the Alpha-Phosphorus Configuration on HIV-1 RT Activity.
Antiviral Res., 117:122-, 2015

PubMed Abstract: The acyclic nucleosides thiophosphonates (9-[2-(thiophosphonomethoxy)ethyl]adenine (S-PMEA) and (R)-9-[2-(thiophosphonomethoxy)propyl]adenine (S-PMPA), exhibit antiviral activity against HIV-1, -2 and HBV. Their diphosphate forms S-PMEApp and S-PMPApp, synthesized as stereoisomeric mixture, are potent inhibitors of wild-type (WT) HIV-1 RT. Understanding HIV-1 RT stereoselectivity, however, awaits resolution of the diphosphate forms into defined stereoisomers. To this aim, thiophosphonate monophosphates S-PMEAp and S-PMPAp were synthesized and used in a stereocontrolled enzyme-catalyzed phosphoryl transfer reaction involving either nucleoside diphosphate kinase (NDPK) or creatine kinase (CK) to obtain thiophosphonate diphosphates as separated isomers. We then quantified substrate preference of recombinant WT HIV-1 RT toward pure stereoisomers using in vitro steady-state kinetic analyses. The crystal structure of a complex between Dictyostelium NDPK and S-PMPApp at 2.32Å allowed to determine the absolute configuration at the α-phosphorus atom in relation to the stereo-preference of studied enzymes. The RP isomer of S-PMPApp and S-PMEApp are the preferred substrate over SP for both NDPK and HIV-1 RT.

PubMed: 25766862
DOI: 10.1016/J.ANTIVIRAL.2015.03.003

Experimental method

X-RAY DIFFRACTION (1.25 Å)