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- PDB-7zl8: NME1 in complex with succinyl-CoA -

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Basic information

Entry
Database: PDB / ID: 7zl8
TitleNME1 in complex with succinyl-CoA
ComponentsNucleoside diphosphate kinase A
KeywordsTRANSFERASE / NME1 / complex / nucleoside diphosphate kinase 1 / succinyl-CoA
Function / homology
Function and homology information


intermediate filament binding / negative regulation of myeloid leukocyte differentiation / Azathioprine ADME / Ribavirin ADME / Interconversion of nucleotide di- and triphosphates / DNA nuclease activity / mammary gland development / nucleoside-diphosphate kinase / gamma-tubulin binding / CTP biosynthetic process ...intermediate filament binding / negative regulation of myeloid leukocyte differentiation / Azathioprine ADME / Ribavirin ADME / Interconversion of nucleotide di- and triphosphates / DNA nuclease activity / mammary gland development / nucleoside-diphosphate kinase / gamma-tubulin binding / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / dTMP biosynthetic process / ribosomal small subunit binding / lactation / 3'-5' exonuclease activity / positive regulation of epithelial cell proliferation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / ruffle membrane / positive regulation of neuron projection development / endocytosis / myelin sheath / nervous system development / single-stranded DNA binding / mitochondrial outer membrane / cell differentiation / early endosome / phosphorylation / negative regulation of gene expression / centrosome / GTP binding / protein kinase binding / perinuclear region of cytoplasm / enzyme binding / magnesium ion binding / mitochondrion / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily
Similarity search - Domain/homology
SUCCINYL-COENZYME A / Nucleoside diphosphate kinase A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsGarcia-Saez, I. / Iuso, D. / Khochbin, S. / Petosa, C.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
CitationJournal: Sci Adv / Year: 2023
Title: Nucleoside diphosphate kinases 1 and 2 regulate a protective liver response to a high-fat diet.
Authors: Iuso, D. / Garcia-Saez, I. / Coute, Y. / Yamaryo-Botte, Y. / Boeri Erba, E. / Adrait, A. / Zeaiter, N. / Tokarska-Schlattner, M. / Jilkova, Z.M. / Boussouar, F. / Barral, S. / Signor, L. / ...Authors: Iuso, D. / Garcia-Saez, I. / Coute, Y. / Yamaryo-Botte, Y. / Boeri Erba, E. / Adrait, A. / Zeaiter, N. / Tokarska-Schlattner, M. / Jilkova, Z.M. / Boussouar, F. / Barral, S. / Signor, L. / Couturier, K. / Hajmirza, A. / Chuffart, F. / Bourova-Flin, E. / Vitte, A.L. / Bargier, L. / Puthier, D. / Decaens, T. / Rousseaux, S. / Botte, C. / Schlattner, U. / Petosa, C. / Khochbin, S.
History
DepositionApr 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase A
B: Nucleoside diphosphate kinase A
C: Nucleoside diphosphate kinase A
D: Nucleoside diphosphate kinase A
E: Nucleoside diphosphate kinase A
F: Nucleoside diphosphate kinase A
G: Nucleoside diphosphate kinase A
H: Nucleoside diphosphate kinase A
I: Nucleoside diphosphate kinase A
J: Nucleoside diphosphate kinase A
K: Nucleoside diphosphate kinase A
L: Nucleoside diphosphate kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,14624
Polymers210,73412
Non-polymers10,41112
Water17,150952
1
A: Nucleoside diphosphate kinase A
B: Nucleoside diphosphate kinase A
C: Nucleoside diphosphate kinase A
D: Nucleoside diphosphate kinase A
E: Nucleoside diphosphate kinase A
F: Nucleoside diphosphate kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,57312
Polymers105,3676
Non-polymers5,2066
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20960 Å2
ΔGint-127 kcal/mol
Surface area35130 Å2
2
G: Nucleoside diphosphate kinase A
H: Nucleoside diphosphate kinase A
I: Nucleoside diphosphate kinase A
J: Nucleoside diphosphate kinase A
K: Nucleoside diphosphate kinase A
L: Nucleoside diphosphate kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,57312
Polymers105,3676
Non-polymers5,2066
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20830 Å2
ΔGint-128 kcal/mol
Surface area34590 Å2
Unit cell
Length a, b, c (Å)53.844, 69.087, 225.127
Angle α, β, γ (deg.)90.000, 89.720, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Nucleoside diphosphate kinase A / NDK A / NDP kinase A / Metastasis inhibition factor NM23 / NDPK-A / Tumor metastatic process- ...NDK A / NDP kinase A / Metastasis inhibition factor NM23 / NDPK-A / Tumor metastatic process-associated protein / nm23-M1


Mass: 17561.199 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: NME1 hexamer in complex with succinyl-CoA. / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nme1, Nm23 / Plasmid: pETM-11
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P15532, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-SCA / SUCCINYL-COENZYME A


Mass: 867.607 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C25H40N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 952 / 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: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 4-10% PEG 1000, 0.1M citric acid pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.96→75.04 Å / Num. obs: 115647 / % possible obs: 97.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 28.36 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.199 / Χ2: 1.02 / Net I/σ(I): 3.1
Reflection shellResolution: 1.96→1.99 Å / Redundancy: 3.4 % / Rmerge(I) obs: 2.325 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 5954 / CC1/2: 0.246 / Χ2: 1.07 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSJan 26, 2018data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: own structure NME1-ADP

Resolution: 1.96→75.04 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 31.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 5728 5.04 %
Rwork0.218 107846 -
obs0.2197 113574 95.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.05 Å2 / Biso mean: 26.9457 Å2 / Biso min: 10.4 Å2
Refinement stepCycle: final / Resolution: 1.96→75.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14593 0 372 952 15917
Biso mean--38.12 27.61 -
Num. residues----1832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-1.980.38142230.37463599382295
1.98-2.010.40451880.36923568375697
2.01-2.030.38462190.373702392198
2.03-2.060.37491720.3683672384499
2.06-2.080.35232140.35683755396999
2.08-2.110.38981990.34743633383299
2.11-2.140.3481910.349538073998100
2.14-2.170.38662010.335736993900100
2.17-2.210.37582320.32473666389899
2.21-2.230.52951110.47151696180773
2.25-2.280.48351010.41632125222679
2.28-2.320.30821960.310337383934100
2.32-2.370.35311850.285837873972100
2.37-2.420.31321980.280336833881100
2.42-2.470.33891760.288638043980100
2.47-2.530.30671720.265336893861100
2.53-2.590.28871880.252238164004100
2.59-2.660.28892120.242437523964100
2.66-2.740.28762140.239437033917100
2.74-2.830.26461800.235937823962100
2.83-2.930.29231870.22537503937100
2.93-3.040.24162070.194137503957100
3.05-3.180.20541990.190937843983100
3.18-3.350.21612020.173137693971100
3.35-3.560.19651980.165637483946100
3.56-3.840.19181650.1633180334583
3.84-4.220.1672200.14053685390599
4.22-4.830.1572190.121937974016100
4.83-6.090.19741550.154238674022100
6.09-75.040.1852040.16173840404498

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