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- PDB-7r4m: Crystal structure of mitochondrial NAD kinase -

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Basic information

Entry
Database: PDB / ID: 7r4m
TitleCrystal structure of mitochondrial NAD kinase
ComponentsNAD kinase 2, mitochondrial
KeywordsTRANSFERASE / NAD kinase
Function / homology
Function and homology information


NAD+ kinase / NAD+ kinase activity / NADP+ biosynthetic process / Nicotinate metabolism / NAD+ metabolic process / Mitochondrial protein degradation / mitochondrial matrix / 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 / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal
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: 2.29 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)45,4733
Polymers44,6891
Non-polymers7832
Water2,738152
1
A: NAD kinase 2, mitochondrial
hetero molecules

A: NAD kinase 2, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,9466
Polymers89,3792
Non-polymers1,5674
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7230 Å2
ΔGint-51 kcal/mol
Surface area29360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.470, 68.470, 223.420
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-627-

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
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.93 Å3/Da / Density % sol: 58.02 %
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: 2.29→50.4 Å / Num. obs: 24750 / % possible obs: 99.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 49.77 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.041 / Rrim(I) all: 0.103 / Net I/σ(I): 11.1 / Num. measured all: 141723 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.29-2.375.61.2191334923660.4960.5371.3421.299.4
8.88-50.44.30.04222035120.9950.0230.04930.296

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.1refinement
Aimless0.7.7data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold

Resolution: 2.29→40.59 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 2047 8.3 %
Rwork0.2005 22619 -
obs0.2039 24666 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 141.43 Å2 / Biso mean: 61.0264 Å2 / Biso min: 34.85 Å2
Refinement stepCycle: final / Resolution: 2.29→40.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2653 0 49 152 2854
Biso mean--44.72 56.72 -
Num. residues----338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.29-2.350.32381530.32041435158899
2.35-2.410.37561490.310514641613100
2.41-2.470.381450.286914761621100
2.47-2.540.27861400.271415031643100
2.54-2.620.29551470.24031440158799
2.62-2.720.30441190.248714881607100
2.72-2.830.29291230.231915021625100
2.83-2.960.28171480.248814821630100
2.96-3.110.25871230.226415321655100
3.11-3.310.24051210.202914951616100
3.31-3.560.25991360.184615251661100
3.56-3.920.20391510.171504165599
3.92-4.490.17311190.148215551674100
4.49-5.650.19651290.15411574170399
5.65-40.590.24981440.22211644178897
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)
16.3516-2.23851.17627.4648-1.89811.9338-0.09830.41570.684-0.0459-0.5919-0.6856-0.30390.92880.52420.3483-0.02130.12790.49280.01810.4546-22.0866-6.307623.9807
26.2317-1.4758-0.38923.60151.64622.50040.176-0.15340.5638-0.2169-0.0368-0.4489-0.31060.4422-0.0930.2895-0.06860.03530.49290.01880.3477-20.1105-9.149630.82
32.09-0.3119-1.22372.58370.86213.1237-0.007-0.1332-0.230.1250.0470.22570.0966-0.0847-0.04760.3511-0.02040.00060.55070.06920.4026-24.9202-21.283230.2181
42.09810.69220.77042.23790.03693.81620.0736-0.0403-0.0844-0.10560.12160.2930.5083-0.4223-0.09460.4205-0.0525-0.05120.4250.06690.4234-22.0094-31.1976.7318
54.3410.01921.73852.6587-3.90096.93510.28160.9753-0.9865-0.75690.27820.44421.3807-0.0508-0.56110.6749-0.0082-0.09710.4803-0.07430.5499-17.2285-35.70160.0391
62.2460.8749-0.6141.9231-0.91353.7092-0.00140.1195-0.0914-0.0338-0.0201-0.06-0.09480.10880.07640.36570.0191-0.02270.39810.00440.4152-12.1717-26.683514.0054
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 65 through 108 )A65 - 108
2X-RAY DIFFRACTION2chain 'A' and (resid 109 through 160 )A109 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 221 )A161 - 221
4X-RAY DIFFRACTION4chain 'A' and (resid 222 through 377 )A222 - 377
5X-RAY DIFFRACTION5chain 'A' and (resid 378 through 402 )A378 - 402
6X-RAY DIFFRACTION6chain 'A' and (resid 403 through 442 )A403 - 442

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