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- PDB-7r4k: Crystal structure of human mitochondrial NAD kinase -

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Basic information

Entry
Database: PDB / ID: 7r4k
TitleCrystal structure of human mitochondrial NAD kinase
ComponentsNAD kinase 2, mitochondrial
KeywordsTRANSFERASE / NADP bound form with Magnesium
Function / homology
Function and homology information


NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / Nicotinate metabolism / NAD metabolic process / Mitochondrial protein degradation / mitochondrial matrix / phosphorylation / protein homodimerization activity / mitochondrion / ATP binding
Similarity search - Function
NAD kinase 2, mitochondrial / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NAD kinase 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.33 Å
AuthorsLabesse, G. / Mary, C. / Gelin, M. / Lionne, C.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE18-0011-01 France
CitationJournal: Mol.Cell / Year: 2022
Title: Crystal structure of human NADK2 reveals a dimeric organization and active site occlusion by lysine acetylation.
Authors: Mary, C. / Soflaee, M.H. / Kesavan, R. / Gelin, M. / Brown, H. / Zacharias, G. / Mathews, T.P. / Lemoff, A. / Lionne, C. / Labesse, G. / Hoxhaj, G.
History
DepositionFeb 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4573
Polymers44,6891
Non-polymers7682
Water1,40578
1
A: NAD kinase 2, mitochondrial
hetero molecules

A: NAD kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9146
Polymers89,3792
Non-polymers1,5354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6840 Å2
ΔGint-41 kcal/mol
Surface area29330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.583, 67.583, 221.815
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-653-

HOH

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Components

#1: Protein NAD kinase 2, mitochondrial / Mitochondrial NAD kinase / NAD kinase domain-containing protein 1 / mitochondrial


Mass: 44689.320 Da / Num. of mol.: 1 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NADK2, C5orf33, MNADK, NADKD1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4G0N4, NAD+ kinase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400 28% v/v, CaCl2 150 mM, 0.1 M Sodium HEPES, 2% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.98→37.09 Å / Num. obs: 18108 / % possible obs: 89 % / Redundancy: 3.379 % / Biso Wilson estimate: 78.32 Å2 / CC1/2: 0.962 / Rmerge(I) obs: 0.276 / Rpim(I) all: 0.153 / Rrim(I) all: 0.319 / Χ2: 0.671 / Net I/av σ(I): 3.9 / Net I/σ(I): 2.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible allMean I/σ(I) obs
2.98-3.163.1262.37928320.20.6712.7587.1
3.16-3.383.1331.53427630.2771.78288.70.68
3.38-3.653.2250.92725590.5421.07390.11.17
3.65-3.993.3560.55423900.7430.6489.32.06
3.99-4.463.4150.36721280.8930.426903.17
4.46-5.143.7110.25419080.9350.29290.24.74
5.14-6.273.750.23916110.9310.27689.75.01
6.27-8.783.6840.13212200.9870.15288.27.61
8.78-37.093.6050.0886970.9870.10287.113.31

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.1-4122refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold

Resolution: 3.33→37.09 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.11 / Phase error: 29.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2868 645 5.01 %
Rwork0.2137 12231 -
obs0.2173 12876 89.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.12 Å2 / Biso mean: 73.7736 Å2 / Biso min: 26.18 Å2
Refinement stepCycle: final / Resolution: 3.33→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2578 0 49 78 2705
Biso mean--54.21 58.71 -
Num. residues----326
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.33-3.590.35251260.2952478260490
3.59-3.950.31421350.23932452258790
3.95-4.520.29671290.212431256090
4.52-5.690.25831300.19372455258590
5.69-37.090.26181250.18712415254088
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.5038-1.6137-1.82096.41311.50653.46950.5935-0.33150.8222-0.4118-0.17180.4376-1.1186-0.2783-0.2660.5944-0.13620.01020.5315-0.18340.5174-23.2773-6.722229.3322
23.4914-2.0791-2.41081.38561.9445.18950.0049-0.42380.03910.0040.1097-0.11890.14730.4476-0.10620.337-0.0111-0.03570.4639-0.00090.5938-16.3911-20.002625.0008
33.74690.0678-0.13663.5082-0.57385.4187-0.32940.1396-0.1293-0.14850.22960.73340.4193-0.7818-0.01330.5481-0.0777-0.07480.41070.01840.6328-26.69-33.08634.9862
44.6484-0.1555-0.64433.00540.46537.7396-0.07090.9633-0.3122-0.37580.0105-0.13680.79140.838-0.08020.37810.0037-0.07920.5214-0.02640.5562-13.0837-29.74978.1603
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 65 through 132 )A65 - 132
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 282 )A133 - 282
3X-RAY DIFFRACTION3chain 'A' and (resid 283 through 377 )A283 - 377
4X-RAY DIFFRACTION4chain 'A' and (resid 378 through 441 )A378 - 441

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