3B1N

Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with ADP-mizoribine

Summary for 3B1N

• Entry DOI: 10.2210/pdb3b1n/pdb
• Related: 3B1O 3B1P 3B1Q 3B1R
• Descriptor: Ribokinase, putative, 5-hydroxy-1-(beta-D-ribofuranosyl)-1H-imidazole-4-carboxamide, ADENOSINE-5'-DIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: rossmann fold, kinase, atp binding, mg binding, nucleoside binding, transferase
• Biological source: Burkholderia thailandensis
• Total number of polymer chains: 2
• Total formula weight: 73013.87

Authors

Yasutake, Y.,Ota, H.,Hino, E.,Sakasegawa, S.,Tamura, T. (deposition date: 2011-07-05, release date: 2011-11-02, Last modification date: 2024-03-13)

Primary citation

Yasutake, Y.,Ota, H.,Hino, E.,Sakasegawa, S.,Tamura, T.
Structures of Burkholderia thailandensis nucleoside kinase: implications for the catalytic mechanism and nucleoside selectivity
Acta Crystallogr.,Sect.D, 67:945-956, 2011

PubMed Abstract: The nucleoside kinase (NK) from the mesophilic Gram-negative bacterium Burkholderia thailandensis (BthNK) is a member of the phosphofructokinase B (Pfk-B) family and catalyzes the Mg(2+)- and ATP-dependent phosphorylation of a broad range of nucleosides such as inosine (INO), adenosine (ADO) and mizoribine (MZR). BthNK is currently used in clinical practice to measure serum MZR levels. Here, crystal structures of BthNK in a ligand-free form and in complexes with INO, INO-ADP, MZR-ADP and AMP-Mg(2+)-AMP are described. The typical homodimeric architecture of Pfk-B enzymes was detected in three distinct conformational states: an asymmetric dimer with one subunit in an open conformation and the other in a closed conformation (the ligand-free form), a closed conformation (the binary complex with INO) and a fully closed conformation (the other ternary and quaternary complexes). The previously unreported fully closed structures suggest the possibility that Mg(2+) might directly interact with the β- and γ-phosphates of ATP to maintain neutralization of the negative charge throughout the reaction. The nucleoside-complex structures also showed that the base moiety of the bound nucleoside is partly exposed to the solvent, thereby enabling the recognition of a wide range of nucleoside bases. Gly170 is responsible for the solvent accessibility of the base moiety and is assumed to be a key residue for the broad nucleoside recognition of BthNK. Remarkably, the G170Q mutation increases the specificity of BthNK for ADO. These findings provide insight into the conformational dynamics, catalytic mechanism and nucleoside selectivity of BthNK and related enzymes.

PubMed: 22101821
DOI: 10.1107/S0907444911038777

Experimental method

X-RAY DIFFRACTION (1.55 Å)