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- PDB-7zve: K403 acetylated glucose-6-phosphate dehydrogenase (G6PD) -

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Basic information

Entry
Database: PDB / ID: 7zve
TitleK403 acetylated glucose-6-phosphate dehydrogenase (G6PD)
Components(Glucose-6-phosphate 1- ...) x 7
KeywordsOXIDOREDUCTASE / Lysine acetylation / metabolic regulation / post-translational modification / genetic code expansion
Function / homology
Function and homology information


negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / glucose-6-phosphate dehydrogenase (NADP+) / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / NADPH regeneration ...negative regulation of protein glutathionylation / pentose biosynthetic process / ribose phosphate biosynthetic process / glucose-6-phosphate dehydrogenase (NADP+) / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / NADPH regeneration / negative regulation of cell growth involved in cardiac muscle cell development / glucose 6-phosphate metabolic process / NADP metabolic process / pentose-phosphate shunt / D-glucose binding / NFE2L2 regulates pentose phosphate pathway genes / response to food / erythrocyte maturation / cholesterol biosynthetic process / centriolar satellite / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / substantia nigra development / glutathione metabolic process / TP53 Regulates Metabolic Genes / response to organic cyclic compound / lipid metabolic process / cytoplasmic side of plasma membrane / glucose metabolic process / NADP binding / cellular response to oxidative stress / response to ethanol / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Glucose-6-phosphate dehydrogenase, active site / Glucose-6-phosphate dehydrogenase active site. / Glucose-6-phosphate dehydrogenase / Glucose-6-phosphate dehydrogenase, NAD-binding / Glucose-6-phosphate dehydrogenase, C-terminal / Glucose-6-phosphate dehydrogenase, NAD binding domain / Glucose-6-phosphate dehydrogenase, C-terminal domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
COPPER (II) ION / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsWu, F. / Muskat, N.H. / Shahar, A. / Arbely, E.
Funding supportEuropean Union, Israel, 2items
OrganizationGrant numberCountry
European Research Council (ERC)678461European Union
Israel Science Foundation1769/20 Israel
CitationJournal: Nat Commun / Year: 2023
Title: Acetylation-dependent coupling between G6PD activity and apoptotic signaling.
Authors: Wu, F. / Muskat, N.H. / Dvilansky, I. / Koren, O. / Shahar, A. / Gazit, R. / Elia, N. / Arbely, E.
History
DepositionMay 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Feb 7, 2024Group: Database references / Category: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase
C: Glucose-6-phosphate 1-dehydrogenase
D: Glucose-6-phosphate 1-dehydrogenase
E: Glucose-6-phosphate 1-dehydrogenase
F: Glucose-6-phosphate 1-dehydrogenase
G: Glucose-6-phosphate 1-dehydrogenase
H: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)459,97017
Polymers459,1708
Non-polymers8009
Water7,170398
1
E: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

A: Glucose-6-phosphate 1-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)115,2813
Polymers115,1892
Non-polymers921
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_456x-1,y,z+11
Buried area6640 Å2
ΔGint-52 kcal/mol
Surface area39150 Å2
MethodPISA
2
B: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

H: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,1566
Polymers114,8162
Non-polymers3404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area6760 Å2
ΔGint-43 kcal/mol
Surface area38990 Å2
MethodPISA
3
D: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

C: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9294
Polymers114,7452
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_465x-1,y+1,z1
Buried area6260 Å2
ΔGint-42 kcal/mol
Surface area39320 Å2
MethodPISA
4
F: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

G: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,6044
Polymers114,4202
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area6100 Å2
ΔGint-36 kcal/mol
Surface area39340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.363, 122.609, 161.310
Angle α, β, γ (deg.)77.23, 80.99, 77.40
Int Tables number1
Space group name H-MP1

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Components

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Glucose-6-phosphate 1- ... , 7 types, 8 molecules ABCDHEFG

#1: Protein Glucose-6-phosphate 1-dehydrogenase


Mass: 57602.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P11413
#2: Protein Glucose-6-phosphate 1-dehydrogenase / G6PD


Mass: 57358.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Production host: Escherichia coli (E. coli)
References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+)
#3: Protein Glucose-6-phosphate 1-dehydrogenase / G6PD


Mass: 57287.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Production host: Escherichia coli (E. coli)
References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+)
#4: Protein Glucose-6-phosphate 1-dehydrogenase / G6PD


Mass: 57457.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Production host: Escherichia coli (E. coli)
References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+)
#5: Protein Glucose-6-phosphate 1-dehydrogenase / G6PD


Mass: 57586.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Production host: Escherichia coli (E. coli)
References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+)
#6: Protein Glucose-6-phosphate 1-dehydrogenase / G6PD


Mass: 57246.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Production host: Escherichia coli (E. coli)
References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+)
#7: Protein Glucose-6-phosphate 1-dehydrogenase


Mass: 57174.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P11413

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Non-polymers , 3 types, 407 molecules

#8: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: obtained synthetically / Formula: H2O

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Details

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: 2.62 Å3/Da / Density % sol: 53.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 5% Tacsimate, 0.1M Hepes pH 7.0 10% PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.28→117.38 Å / Num. obs: 205547 / % possible obs: 97 % / Redundancy: 6.5 % / CC1/2: 0.992 / Rpim(I) all: 0.112 / Net I/σ(I): 5
Reflection shellResolution: 2.28→2.32 Å / Num. unique obs: 10178 / CC1/2: 0.313

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QKI

1qki


Resolution: 2.28→50.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.93 / SU B: 29.972 / SU ML: 0.296 / Cross valid method: THROUGHOUT / ESU R: 0.354 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26098 10329 5 %RANDOM
Rwork0.21068 ---
obs0.21319 195116 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20.02 Å2-0.15 Å2
2--0.76 Å2-0.96 Å2
3----0.87 Å2
Refinement stepCycle: 1 / Resolution: 2.28→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32357 0 1 398 32756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01233117
X-RAY DIFFRACTIONr_bond_other_d0.0010.01629994
X-RAY DIFFRACTIONr_angle_refined_deg2.0491.64244723
X-RAY DIFFRACTIONr_angle_other_deg0.6951.55369941
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.23353971
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.0229.893280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.372105748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0990.24775
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0237939
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026854
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2513.99715939
X-RAY DIFFRACTIONr_mcbond_other5.2513.99715939
X-RAY DIFFRACTIONr_mcangle_it7.2295.99219880
X-RAY DIFFRACTIONr_mcangle_other7.2295.99219881
X-RAY DIFFRACTIONr_scbond_it6.5984.43617178
X-RAY DIFFRACTIONr_scbond_other6.5984.43617179
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.0536.46624841
X-RAY DIFFRACTIONr_long_range_B_refined10.78560.55735314
X-RAY DIFFRACTIONr_long_range_B_other10.78860.29435283
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.283→2.342 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 758 -
Rwork0.361 14395 -
obs--97.31 %
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)
10.35520.22280.1380.37590.28891.69570.0034-0.0214-0.1050.0838-0.03460.03030.1802-0.07210.03120.04190.01050.01570.0875-0.06350.1159-13.7454-7.2295-40.0343
20.663-0.4858-0.09651.1948-0.27780.47730.01070.12570.0468-0.1564-0.0451-0.0384-0.0687-0.00110.03440.0793-0.0138-0.02160.0945-0.04710.0655-38.6102-24.93170.9475
30.58940.35290.20941.08350.62341.04810.0461-0.1633-0.13440.2479-0.05210.01180.1332-0.03580.0060.0594-0.00120.0130.1025-0.01810.10633.0845-44.756436.1167
40.63160.03790.05061.687-0.11630.418-0.0484-0.1589-0.08540.1783-0.00070.04170.08440.02210.04910.04850.02150.02690.0926-0.02780.082-9.032831.634813.2944
50.52260.41410.30331.65430.25210.6460.0779-0.1729-0.12980.22050.0035-0.10270.27790.0284-0.08140.14480.0507-0.01930.1896-0.03740.1066-27.582-12.663983.5058
60.4615-0.2472-0.24080.30790.18351.75680.06880.01750.1498-0.108-0.05890.0193-0.167-0.1256-0.00990.06320.0062-0.01440.0971-0.06240.12714.526713.366552.7812
70.674-0.4711-0.25641.29170.08240.65570.04620.17140.2061-0.1968-0.0032-0.1518-0.33130.0744-0.0430.2317-0.0876-0.0160.2234-0.05080.1658-31.040752.150287.7337
80.6012-0.4302-0.21780.71620.52231.19820.06060.16440.0738-0.2598-0.04270.0423-0.1261-0.0136-0.01790.1322-0.0185-0.060.1263-0.0380.1283-31.524849.2281-23.3102
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 505
2X-RAY DIFFRACTION2B6 - 602
3X-RAY DIFFRACTION3C7 - 601
4X-RAY DIFFRACTION4D5 - 601
5X-RAY DIFFRACTION5E5 - 601
6X-RAY DIFFRACTION6F7 - 601
7X-RAY DIFFRACTION7G8 - 601
8X-RAY DIFFRACTION8H5 - 601

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