9RVW

Crystal structure of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae

Summary for 9RVW

• Entry DOI: 10.2210/pdb9rvw/pdb
• Related: 9sfo
• Descriptor: Nucleoside diphosphate kinase (2 entities in total)
• Functional Keywords: hexamer, soluble protein, kinase, transferase
• Biological source: Streptococcus pneumoniae R6
• Total number of polymer chains: 1
• Total formula weight: 17266.55

Authors

Kaplan, E.,Kerboeuf, J.,Gonzalez, C.,Ballut, L.,Jault, J.-M. (deposition date: 2025-07-09, release date: 2026-07-22, Last modification date: 2026-08-19)

Primary citation

Kerboeuf, J.,Nouri, P.,Galisson, F.,Daury, L.,Giraud, M.F.,Lambert, O.,Orelle, C.,Ballut, L.,Kaplan, E.,Jault, J.M.,Gonzalez, C.
Quaternary structures of Streptococcus pneumoniae nucleoside diphosphate kinase: From hexamers to supramolecular assemblies.
Protein Sci., 35:e70735-e70735, 2026

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 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.

PubMed: 42568346
DOI: 10.1002/pro.70735

Experimental method

X-RAY DIFFRACTION (1.2 Å)