Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Quaternary structures of Streptococcus pneumoniae nucleoside diphosphate kinase: From hexamers to supramolecular assemblies.
Journal, issue, pages	Protein Sci, Vol. 35, Issue 9, Page e70735, Year 2026
Publish date	Aug 8, 2026
Authors	Julie Kerboeuf / Paul Nouri / Frédéric Galisson / Laetitia Daury / Marie-France Giraud / Olivier Lambert / Cédric Orelle / Lionel Ballut / Elise Kaplan / Jean-Michel Jault / Cécile Gonzalez /
PubMed Abstract	The nucleoside diphosphate kinase (NDK) is a key enzyme that controls the balance of nucleotide pools in all living organisms. Beyond this fundamental role, NDKs exert pleiotropic effects in many ...The nucleoside diphosphate kinase (NDK) is a key enzyme that controls the balance of nucleotide pools in all living organisms. Beyond this fundamental role, NDKs exert pleiotropic effects in many cellular processes, including cell development, signal transduction, differentiation, tumor metastasis, and gene expression. The quaternary structure of NDK is typically hexameric-organized as a trimer of dimers in eukaryotic cells and in many prokaryotes-though in some species it can also be tetrameric. Here, we report the crystal structure of Streptococcus pneumoniae NDK (SpNDK) in its apo state (1.2 Å) and in an adenosine diPhosphate (ADP)-vanadate-bound state (3.4 Å). In both structures, SpNDK adopts a hexameric assembly and the fold of each monomer is highly conserved compared to NDKs from other organisms. A notable feature is the extended Kpn-loop, which plays a key role in stabilizing the hexamer. The protein exhibited remarkably high thermal stability (T ~ 76°C). However, mutation of R28 (R28A), which interacts with the Kpn-loop, destabilized the hexamer, lowering the T by >20°C. Unexpectedly, size-exclusion chromatography and mass photometry revealed that wild-type SpNDK exists as an equilibrium mixture of hexamers, dodecamers, and higher-order supramolecular assemblies. Using cryo-electron microscopy, we solved the three Dimensional (3D) structure of the hexameric state at 2.47 Å resolution, and resolved dodecameric assemblies of the protein. Since the oligomeric state of the NDK influences its cellular function, further investigations will be needed to address the in vivo relevance of these findings, in line with the broad and multifaceted roles of this enzyme family.
External links	Protein Sci / PubMed:42568346 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.2 - 4.09 Å
Structure data	EMDB-55333: CryoEM structure of nucleoside diphosphate kinase (NDK) dodecamer 2 from Streptococcus pneumoniae Method: EM (single particle) / Resolution: 3.81 Å EMDB-55334: CryoEM structure of nucleoside diphosphate kinase (NDK) dodecamer 1 from Streptococcus pneumoniae Method: EM (single particle) / Resolution: 4.09 Å PDB-9rvw: Crystal structure of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae Method: X-RAY DIFFRACTION / Resolution: 1.2 Å PDB-9sfo: Crystal structure of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae in complex with ADP and vanadate Method: X-RAY DIFFRACTION / Resolution: 3.42 Å
Chemicals	ChemComp-HOH: WATER ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-VN4: oxido(dioxo)vanadium ChemComp-MG: Unknown entry ChemComp-VO4*: VANADATE ION
Source	streptococcus pneumoniae r6 (bacteria)
Keywords	TRANSFERASE / Hexamer / soluble protein / kinase