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- PDB-9rvw: Crystal structure of nucleoside diphosphate kinase (NDK) from Str... -

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Basic information

Entry
Database: PDB / ID: 9rvw
TitleCrystal structure of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Hexamer / soluble protein / kinase
Function / homology
Function and homology information


purine nucleotide metabolic process / pyrimidine nucleotide metabolic process / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily
Similarity search - Domain/homology
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKaplan, E. / Kerboeuf, J. / Gonzalez, C. / Ballut, L. / Jault, J.-M.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Protein Sci / Year: 2026
Title: Quaternary structures of Streptococcus pneumoniae nucleoside diphosphate kinase: From hexamers to supramolecular assemblies.
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 /
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.
History
DepositionJul 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)17,2671
Polymers17,2671
Non-polymers00
Water3,135174
1
A: Nucleoside diphosphate kinase
x 6


Theoretical massNumber of molelcules
Total (without water)103,5996
Polymers103,5996
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area10440 Å2
ΔGint-55 kcal/mol
Surface area34400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.878, 68.878, 156.407
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-362-

HOH

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Components

#1: Protein Nucleoside diphosphate kinase / NDK / NDP kinase / Nucleoside-2-P kinase


Mass: 17266.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Gene: ndk, spr1775 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P65537, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.51 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M calcium chloride dihydrate, 0.1 M HEPES sodium pH 7.5 and 28% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.2→34.44 Å / Num. obs: 44110 / % possible obs: 98.1 % / Redundancy: 10.4 % / CC1/2: 0.994 / Net I/σ(I): 13.5
Reflection shellResolution: 1.2→1.22 Å / Num. unique obs: 1749 / CC1/2: 0.794

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→34.44 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.571 / SU ML: 0.026 / Cross valid method: FREE R-VALUE / ESU R: 0.039 / ESU R Free: 0.039
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1853 2156 4.888 %
Rwork0.1724 41954 -
all0.173 --
obs-44110 98.029 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.978 Å2
Baniso -1Baniso -2Baniso -3
1-0.305 Å20.153 Å20 Å2
2--0.305 Å20 Å2
3----0.99 Å2
Refinement stepCycle: LAST / Resolution: 1.2→34.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 0 174 1262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0121110
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161066
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.8421497
X-RAY DIFFRACTIONr_angle_other_deg0.6671.7642459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7315136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.25259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.62910200
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.1821053
X-RAY DIFFRACTIONr_chiral_restr0.1120.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02256
X-RAY DIFFRACTIONr_nbd_refined0.2420.2221
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.2976
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2554
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2604
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2570.2104
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1130.29
X-RAY DIFFRACTIONr_nbd_other0.1550.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.225
X-RAY DIFFRACTIONr_mcbond_it1.6141.187547
X-RAY DIFFRACTIONr_mcbond_other1.5931.185547
X-RAY DIFFRACTIONr_mcangle_it2.4652.132682
X-RAY DIFFRACTIONr_mcangle_other2.482.135683
X-RAY DIFFRACTIONr_scbond_it2.7071.53563
X-RAY DIFFRACTIONr_scbond_other2.7051.531564
X-RAY DIFFRACTIONr_scangle_it4.1312.662815
X-RAY DIFFRACTIONr_scangle_other4.1292.662816
X-RAY DIFFRACTIONr_lrange_it5.3713.8731317
X-RAY DIFFRACTIONr_lrange_other5.12312.7361268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.2221490.2522553X-RAY DIFFRACTION81.6068
1.231-1.2650.221580.2162840X-RAY DIFFRACTION93.8929
1.265-1.3020.221680.1992950X-RAY DIFFRACTION100
1.302-1.3420.2281450.1932856X-RAY DIFFRACTION100
1.342-1.3850.2231480.1892807X-RAY DIFFRACTION100
1.385-1.4340.1711540.1682698X-RAY DIFFRACTION100
1.434-1.4880.1731470.1552609X-RAY DIFFRACTION100
1.488-1.5490.161990.1472530X-RAY DIFFRACTION99.924
1.549-1.6170.1891180.1532428X-RAY DIFFRACTION99.9607
1.617-1.6960.1741050.1532336X-RAY DIFFRACTION100
1.696-1.7880.1971380.1542163X-RAY DIFFRACTION100
1.788-1.8960.1681190.1522098X-RAY DIFFRACTION99.9549
1.896-2.0260.165910.1551949X-RAY DIFFRACTION97.9357
2.026-2.1880.167830.1481813X-RAY DIFFRACTION98.2893
2.188-2.3960.169820.151702X-RAY DIFFRACTION100
2.396-2.6770.179780.1571544X-RAY DIFFRACTION100
2.677-3.0880.177580.161391X-RAY DIFFRACTION100
3.088-3.7740.189550.1671176X-RAY DIFFRACTION100
3.774-5.3060.164520.176932X-RAY DIFFRACTION100
5.306-34.440.52590.355579X-RAY DIFFRACTION100

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