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

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Basic information

Entry
Database: PDB / ID: 9sfo
TitleCrystal structure of nucleoside diphosphate kinase (NDK) from Streptococcus pneumoniae in complex with ADP and vanadate
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
ADENOSINE-5'-DIPHOSPHATE / oxido(dioxo)vanadium / VANADATE ION / Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsBallut, L. / Gonzalez, C. / Kaplan, E. / Kerboeuf, J. / Jault, J.-M.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE11-0018 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
DepositionAug 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,48919
Polymers99,1726
Non-polymers2,31713
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14090 Å2
ΔGint-115 kcal/mol
Surface area34150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.830, 198.830, 72.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 16528.742 Da / Num. of mol.: 6
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: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-VN4 / oxido(dioxo)vanadium


Mass: 98.940 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O3V / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O4V / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 3.6 Å3/Da / Density % sol: 65.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 24% PEG 3350, 100 mM MES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 3.42→72.28 Å / Num. obs: 20087 / % possible obs: 99.7 % / Redundancy: 5.8 % / CC1/2: 0.914 / Rmerge(I) obs: 0.376 / Rpim(I) all: 0.165 / Rrim(I) all: 0.412 / Χ2: 1.04 / Net I/σ(I): 4.5 / Num. measured all: 116947
Reflection shellResolution: 3.42→3.69 Å / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.978 / Num. measured all: 24602 / Num. unique obs: 4041 / CC1/2: 0.802 / Rpim(I) all: 0.419 / Rrim(I) all: 1.068 / Χ2: 1.2 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.42→70.396 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.834 / SU B: 28.853 / SU ML: 0.431 / Cross valid method: THROUGHOUT / ESU R Free: 0.558
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2688 1027 5.134 %RANDOM
Rwork0.204 18978 --
all0.207 ---
obs-20005 99.231 %-
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: 64.535 Å2
Baniso -1Baniso -2Baniso -3
1-2.019 Å20 Å20 Å2
2--2.019 Å2-0 Å2
3----4.038 Å2
Refinement stepCycle: LAST / Resolution: 3.42→70.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6588 0 133 0 6721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0126852
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166514
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.8449258
X-RAY DIFFRACTIONr_angle_other_deg0.4891.76115030
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5935824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.899554
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.05154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.945101216
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.47810320
X-RAY DIFFRACTIONr_chiral_restr0.0660.21011
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027988
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021560
X-RAY DIFFRACTIONr_nbd_refined0.2160.21403
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.26088
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23286
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.23624
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2130
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0390.23
X-RAY DIFFRACTIONr_metal_ion_refined0.2020.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.23
X-RAY DIFFRACTIONr_nbd_other0.1860.224
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1710.22
X-RAY DIFFRACTIONr_mcbond_it4.3856.213314
X-RAY DIFFRACTIONr_mcbond_other4.3846.213314
X-RAY DIFFRACTIONr_mcangle_it7.30411.1564132
X-RAY DIFFRACTIONr_mcangle_other7.30311.1574133
X-RAY DIFFRACTIONr_scbond_it4.6326.813538
X-RAY DIFFRACTIONr_scbond_other4.6266.813535
X-RAY DIFFRACTIONr_scangle_it7.8912.3365126
X-RAY DIFFRACTIONr_scangle_other7.88612.3335124
X-RAY DIFFRACTIONr_lrange_it11.40157.3757434
X-RAY DIFFRACTIONr_lrange_other11.457.3967435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.42-3.5090.319770.22613630.23114440.9250.96399.7230.214
3.509-3.6050.33770.31613370.31714190.9180.91699.64760.307
3.605-3.7090.561690.51612810.51813710.7830.83898.46830.522
3.709-3.8230.329670.32912640.32913620.930.93197.72390.322
3.823-3.9480.332670.21912090.22412810.9270.96699.60970.21
3.948-4.0860.266790.18512030.19112880.9510.97599.53420.177
4.086-4.2390.257580.1611680.16412300.9550.98299.67480.158
4.239-4.4120.209500.15611110.15811670.9670.98399.48590.156
4.412-4.6070.214610.13310730.13711380.9710.98899.64850.134
4.607-4.8310.21610.12110330.12510960.9770.9999.81750.125
4.831-5.0910.193450.1239840.12610320.9750.9999.70930.127
5.091-5.3980.199550.1449220.1479820.970.98999.49080.146
5.398-5.7680.226450.158860.1539360.9710.98799.46580.154
5.768-6.2270.28410.1638190.1688730.9530.98498.51090.171
6.227-6.8160.268430.1597600.1658110.9460.98299.01360.171
6.816-7.6120.211300.1486950.1517360.9720.98498.50540.162
7.612-8.7720.205400.1246230.1286670.970.98999.40030.14
8.772-10.7020.22250.1455420.1485710.9670.98799.29950.167
10.702-14.9630.172290.1824250.1814580.9850.98299.12660.215
14.963-70.3960.31580.4762800.4692950.9790.7997.62711.429

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