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- PDB-7seh: Glucose-6-phosphate 1-dehydrogenase (K403QdLtL) -

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Basic information

Entry
Database: PDB / ID: 7seh
TitleGlucose-6-phosphate 1-dehydrogenase (K403QdLtL)
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Glucose-6-phosphate 1-dehydrogenase / dimer-tetramer locked
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 / pentose-phosphate shunt, oxidative branch / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / 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 / pentose-phosphate shunt, oxidative branch / glucose-6-phosphate dehydrogenase activity / response to iron(III) ion / Pentose phosphate pathway / NADPH regeneration / negative regulation of cell growth involved in cardiac muscle cell development / glucose 6-phosphate metabolic process / NADP metabolic process / pentose-phosphate shunt / glucose binding / NFE2L2 regulates pentose phosphate pathway genes / response to food / cholesterol biosynthetic process / erythrocyte maturation / centriolar satellite / negative regulation of reactive oxygen species metabolic process / glutathione metabolic process / regulation of neuron apoptotic process / substantia nigra development / TP53 Regulates Metabolic Genes / lipid metabolic process / cytoplasmic side of plasma membrane / response to organic cyclic compound / glucose metabolic process / cellular response to oxidative stress / NADP binding / response to ethanol / intracellular membrane-bounded organelle / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / cytosol / cytoplasm
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMathews, I.I. / Garcia, A.A. / Wakatsuki, S. / Mochly-Rosen, D.
Funding support United States, 5items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)HD084422 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133894 United States
National Science Foundation (NSF, United States)1656518 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM113854 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Stabilization of glucose-6-phosphate dehydrogenase oligomers enhances catalytic activity and stability of clinical variants.
Authors: Garcia, A.A. / Mathews, I.I. / Horikoshi, N. / Matsui, T. / Kaur, M. / Wakatsuki, S. / Mochly-Rosen, D.
History
DepositionSep 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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: Glucose-6-phosphate 1-dehydrogenase
B: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,2474
Polymers119,7602
Non-polymers1,4872
Water64936
1
A: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)121,2474
Polymers119,7602
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x+1/2,-y-1,z+1/21
Buried area5020 Å2
ΔGint-27 kcal/mol
Surface area37180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.640, 87.860, 160.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glucose-6-phosphate 1-dehydrogenase / G6PD


Mass: 59880.223 Da / Num. of mol.: 2 / Mutation: A277C, K403Q, C516 insertion at C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Plasmid: pET-28a (+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C43
References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+)
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 2,2'-disulfanediylbis(N-(2-(1H-indol-3-yl)ethyl)ethan-1-amine), NADP+, MES, PEG4000, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2021 / Details: Flat Si Rh coated Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.9→38.99 Å / Num. obs: 24109 / % possible obs: 99.9 % / Redundancy: 13.062 % / Biso Wilson estimate: 79.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.199 / Rrim(I) all: 0.208 / Χ2: 0.812 / Net I/σ(I): 13.71 / Num. measured all: 314920 / Scaling rejects: 47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.9-2.9813.5812.8661.5123929176217620.6712.978100
2.98-3.0613.4242.2251.9322781169716970.7772.314100
3.06-3.1512.9861.92.3621778167716770.8041.978100
3.15-3.2412.0531.4013.1619501161816180.8841.464100
3.24-3.3513.0911.0064.5620395155815580.931.047100
3.35-3.4714.060.7935.9221441152715250.9520.82399.9
3.47-3.613.9830.6237.1620569147114710.9710.647100
3.6-3.7413.870.4669.4819612141514140.9820.48499.9
3.74-3.9113.7440.33411.9918595135413530.990.34799.9
3.91-4.113.5660.23815.0617758130913090.9950.248100
4.1-4.3213.2020.18717.3216370124112400.9960.19499.9
4.32-4.5912.3090.1419.9114525118011800.9970.147100
4.59-4.911.5040.1122.5312861111811180.9980.115100
4.9-5.2913.4250.11323.6513975104110410.9980.118100
5.29-5.813.3640.10824.07129909729720.9980.112100
5.8-6.4813.1420.10324.93113818678660.9980.10799.9
6.48-7.4912.3310.06630.4396927867860.9990.068100
7.49-9.1710.9360.04340.1174046776770.9990.045100
9.17-12.9711.4630.02957.72614453653610.03100
12.97-38.9910.4170.03157.7732193233090.9990.03395.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6va7

6va7


Resolution: 2.9→38.99 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.89 / SU B: 23.469 / SU ML: 0.425 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3018 1206 5 %RANDOM
Rwork0.2058 ---
obs0.2106 22903 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 179.41 Å2 / Biso mean: 77.492 Å2 / Biso min: 23.96 Å2
Baniso -1Baniso -2Baniso -3
1-3.85 Å2-0 Å20 Å2
2---2.64 Å20 Å2
3----1.2 Å2
Refinement stepCycle: final / Resolution: 2.9→38.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7158 0 96 37 7291
Biso mean--104.41 62.47 -
Num. residues----885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0137422
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176983
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.64810051
X-RAY DIFFRACTIONr_angle_other_deg1.1451.58116035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0015878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.08821.597432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.517151276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1151562
X-RAY DIFFRACTIONr_chiral_restr0.0630.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028369
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021813
LS refinement shellResolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 88 -
Rwork0.339 1668 -
all-1756 -
obs--100 %

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