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- PDB-5ukw: Crystal structure of human Glucose 6-phosphate Dehydrogenase muta... -

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Basic information

Entry
Database: PDB / ID: 5ukw
TitleCrystal structure of human Glucose 6-phosphate Dehydrogenase mutant (A277C) complexed with G6P
ComponentsGlucose-6-phosphate 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase / A277C / Tetramer
Function / homology
Function and homology information


pentose biosynthetic process / ribose phosphate biosynthetic process / response to iron(III) ion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / negative regulation of cell growth involved in cardiac muscle cell development / glucose 6-phosphate metabolic process ...pentose biosynthetic process / ribose phosphate biosynthetic process / response to iron(III) ion / positive regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / glucose-6-phosphate dehydrogenase (NADP+) / glucose-6-phosphate dehydrogenase activity / Pentose phosphate pathway / pentose-phosphate shunt, oxidative branch / 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 / Oxidoreductases / cholesterol biosynthetic process / response to food / erythrocyte maturation / negative regulation of reactive oxygen species metabolic process / substantia nigra development / regulation of neuron apoptotic process / TP53 Regulates Metabolic Genes / lipid metabolic process / glutathione metabolic process / cytoplasmic side of plasma membrane / glucose metabolic process / centriolar satellite / NADP binding / cellular response to oxidative stress / response to ethanol / protein homodimerization activity / extracellular exosome / membrane / identical protein binding / 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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-glucopyranose / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsRanzani, A.T. / Cordeiro, A.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2012/23682-7 Brazil
CitationJournal: FEBS Lett. / Year: 2017
Title: Mutations in the tetramer interface of human glucose-6-phosphate dehydrogenase reveals kinetic differences between oligomeric states.
Authors: Ranzani, A.T. / Cordeiro, A.T.
History
DepositionJan 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucose-6-phosphate 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5543
Polymers56,2021
Non-polymers3522
Water36020
1
A: Glucose-6-phosphate 1-dehydrogenase
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)226,21712
Polymers224,8084
Non-polymers1,4098
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area17170 Å2
ΔGint-95 kcal/mol
Surface area71400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.099, 177.817, 216.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

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


Mass: 56201.934 Da / Num. of mol.: 1 / Fragment: UNP residues 59-541 / Mutation: Q28F, A277C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: G6PD / Plasmid: pET-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+)
#2: Sugar ChemComp-BG6 / 6-O-phosphono-beta-D-glucopyranose / BETA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-beta-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 100 mM Tris-HCl pH 9, 200 mM MgCl2, 13% PEG 4000 and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97643 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97643 Å / Relative weight: 1
ReflectionResolution: 2.65→46.23 Å / Num. obs: 16889 / % possible obs: 100 % / Redundancy: 9.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.05 / Net I/σ(I): 17.2
Reflection shellResolution: 2.65→2.78 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.532 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BH9

2bh9


Resolution: 2.65→46.23 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / Cross valid method: THROUGHOUT / ESU R: 1.531 / ESU R Free: 0.311 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23368 839 5 %RANDOM
Rwork0.18875 ---
obs0.19101 16047 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 58.671 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å2-0 Å2-0 Å2
2--0.24 Å20 Å2
3----2.31 Å2
Refinement stepCycle: 1 / Resolution: 2.65→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3862 0 22 20 3904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193975
X-RAY DIFFRACTIONr_bond_other_d00.023766
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.9585370
X-RAY DIFFRACTIONr_angle_other_deg3.59538654
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9035474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6423.632201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.13215690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4931532
X-RAY DIFFRACTIONr_chiral_restr0.1070.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214474
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02960
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_it3.8165.6341902
X-RAY DIFFRACTIONr_mcbond_other3.8155.6321901
X-RAY DIFFRACTIONr_mcangle_it5.8188.4422374
X-RAY DIFFRACTIONr_mcangle_other5.8178.4442375
X-RAY DIFFRACTIONr_scbond_it4.2736.0582072
X-RAY DIFFRACTIONr_scbond_other4.2716.0582072
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6888.9072997
X-RAY DIFFRACTIONr_long_range_B_refined10.4116543
X-RAY DIFFRACTIONr_long_range_B_other10.4116543
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 50 -
Rwork0.338 1183 -
obs--99.84 %

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