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- PDB-1qki: X-RAY STRUCTURE OF HUMAN GLUCOSE 6-PHOSPHATE DEHYDROGENASE (VARIA... -

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Entry
Database: PDB / ID: 1qki
TitleX-RAY STRUCTURE OF HUMAN GLUCOSE 6-PHOSPHATE DEHYDROGENASE (VARIANT CANTON R459L) COMPLEXED WITH STRUCTURAL NADP+
ComponentsGLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / OXIDOREDUTASE / (CHOH(D)-NADP) / GLUCOSE METABOLISM
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 / NADPH regeneration ...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 / NADPH regeneration / 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 / negative regulation of reactive oxygen species metabolic process / regulation of neuron apoptotic process / glutathione metabolic process / substantia nigra development / TP53 Regulates Metabolic Genes / lipid metabolic process / centriolar satellite / 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 / 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
GLYCOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Glucose-6-phosphate 1-dehydrogenase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAu, S.W.N. / Gover, S. / Lam, V.M.S. / Adams, M.J.
Citation
Journal: Structure / Year: 2000
Title: Human Glucose-6-Phosphate Dehydrogenase: The Crystal Structure Reveals a Structural Nadp+ Molecule and Provides Insights Into Enzyme Deficiency
Authors: Au, S.W.N. / Gover, S. / Lam, V.M.S. / Adams, M.J.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Solution of the Structure of Tetrameric Human Glucose 6-Phosphate Dehydrogenase by Molecular Replacement
Authors: Au, S.W.N. / Naylor, C.E. / Gover, S. / Vandeputte-Rutten, L. / Scopes, D.A. / Mason, P.J. / Luzzatto, L. / Lam, V.M.S. / Adams, M.J.
History
DepositionJul 20, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.date_author_approval / _pdbx_database_status.recvd_author_approval
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 650 HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO THE 2.0A LEUCONOSTOC ... HELIX DETERMINATION METHOD: PROCHECK, WITH IDENTIFICATION CORRESPONDING TO THE 2.0A LEUCONOSTOC MESENTERODES STRUCTURE, 1DPG. THE BEND AT LYS 47 IN HELIX A OF ALL SUBUNITS IS A CONSEQUENCE OF THE CONSERVED PRO 50.
Remark 700 SHEET DETERMINATION METHOD: PROCHECK WITH EXTENSION TAKEN WHERE HYDROGEN BONDING INDICATES THAT ... SHEET DETERMINATION METHOD: PROCHECK WITH EXTENSION TAKEN WHERE HYDROGEN BONDING INDICATES THAT THIS IS APPROPRIATE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)480,35529
Polymers473,3398
Non-polymers7,01621
Water99155
1
A: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
B: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
C: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
D: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,22415
Polymers236,6694
Non-polymers3,55411
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15740 Å2
ΔGint-84.4 kcal/mol
Surface area96080 Å2
MethodPQS
2
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)240,13114
Polymers236,6694
Non-polymers3,46210
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15380 Å2
ΔGint-105.1 kcal/mol
Surface area95420 Å2
MethodPQS
Unit cell
Length a, b, c (Å)128.900, 208.700, 214.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.14549, -0.92776, 0.34365), (-0.92008, -0.25457, -0.29775), (0.36372, -0.27286, -0.89065)49.754, 128.18, 173.244
2given(-0.91411, -0.0304, -0.40432), (-0.0722, -0.96904, 0.2361), (-0.39899, 0.24502, 0.88362)53.47, 129.848, -4.698
3given(-0.22155, 0.97191, 0.07946), (0.97197, 0.21353, 0.09835), (0.07862, 0.09903, -0.99197)-68.504, 42.807, 154.884
4given(0.97915, 0.20146, 0.0261), (0.20045, -0.97901, 0.03695), (0.03299, -0.03095, -0.99898)-23.589, 190.875, 222.52
5given(-0.12197, 0.89405, -0.43104), (-0.94832, 0.0232, 0.31647), (0.29294, 0.44736, 0.84502)-40.408, 34.646, -91.476
6given(-0.89971, -0.10821, 0.42286), (-0.24832, 0.92363, -0.29198), (-0.35896, -0.3677, -0.85787)-31.183, 4.267, 247.829
7given(0.05034, -0.99856, -0.01883), (0.99569, 0.05165, -0.07707), (0.07793, -0.01487, 0.99685)135.148, 76.056, -54.831
8given(0.14373, -0.92089, 0.36237), (-0.92033, -0.25898, -0.29311), (0.36377, -0.29137, -0.88475)47.866, 127.989, 173.92
9given(-0.90588, -0.03619, -0.42199), (-0.06349, -0.97348, 0.21977), (-0.41875, 0.22588, 0.87956)55.326, 131.715, -3.299
10given(-0.23201, 0.97082, 0.06069), (0.97042, 0.22672, 0.08298), (0.0668, 0.07815, -0.9947)-66.934, 42.484, 157.81
11given(0.97288, 0.23064, -0.01778), (0.23132, -0.97033, 0.07035), (-0.00103, -0.07255, -0.99736)-21.219, 184.471, 229.011
12given(-0.09313, 0.8954, -0.43542), (-0.95276, 0.04683, 0.30009), (0.28909, 0.4428, 0.84874)-40.213, 33.193, -91
13given(-0.88871, -0.13393, 0.43848), (-0.27936, 0.91652, -0.28626), (-0.36354, -0.3769, -0.85193)-30.053, 3.506, 248.243
14given(0.02103, -0.99969, 0.0133), (0.99609, 0.0198, -0.08616), (0.08587, 0.01506, 0.99619)130.997, 80.357, -57.424
DetailsTHERE ARE TWO TETRAMERS ABCD AND EFGH IN THE ASYMMETRICUNIT; THESE ARE RELATED BY NON-CRYSTALLOGRAPHY SYMMETRY.DUE TO THE DIFFERENCE OF HINGE ANGLE IN EVERY SUBUNIT, TWOMATRICES ARE PROVIDED TO GENERATE A WHOLE SUBUNIT - ONEFOR THE COENZYME DOMAIN (RESIDUES 31- 200) AND ANOTHER FORTHE LARGE DOMAIN (RESIDUE 201 -511). PRO 172 IS ONLY INTHE CIS CONFORMATION IN SUBUNIT E.

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Components

#1: Protein
GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE / G6PD


Mass: 59167.367 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Gene: G6PD / Plasmid: PTRC99A/G6PDR459L / Gene (production host): G6PD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DF213
References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+)
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID


Mass: 76.051 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H4O3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAS ALL THE EIGHT SUBUNITS ARE VERY SIMILAR, ONLY THE SALT BRIDGES WITHIN SUBUNIT A AND WITHIN ...AS ALL THE EIGHT SUBUNITS ARE VERY SIMILAR, ONLY THE SALT BRIDGES WITHIN SUBUNIT A AND WITHIN SUBUNIT E ARE GIVEN. FOR DETAILS OF RESIDUES FORMING INTERSUBUNIT BRIDGES, SEE JRNL REFERENCE.
Source detailsTHE G6PD PROTEIN USED IN THIS WORK IS THE NATURAL VARIANT ARG459 -> LEU (CANTON, CLASS II, FREQUENT IN CHINA).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.5 % / Description: 3 DATA SETS WERE MERGED, SEE REFERENCE 1.
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.8
Details: HANGING DROP VAPOUR DIFFUSION. 1+1 MICROLITER DROPS IN THE WELL 0.1M SODIUM CITRATE, 0.05M GLYCOLIC ACID, PH 5.8. PROTEIN CONCENTRATION 10MG/ML
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: used microseeding, Au, S.W.N., (1999) Acta Crystallogr.,Sect.D, 55, 826.
pH: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.100 mMNADP+1drop
210 mg/mlprotein1drop
30.1 Msodium citrate1reservoir
40.05 Mglycolic acid1reservoirpH5.8
510-15 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.870, 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1997 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
21.4881
ReflectionResolution: 3→25 Å / Num. obs: 98864 / % possible obs: 85.3 % / Observed criterion σ(I): 4 / Redundancy: 2.2 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 5.2
Reflection shellResolution: 3→3.2 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.565 / % possible all: 74.7
Reflection
*PLUS
Num. measured all: 647973
Reflection shell
*PLUS
Lowest resolution: 3.05 Å / % possible obs: 72 % / Rmerge(I) obs: 0.565

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALAdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DPG

1dpg


Resolution: 3→25 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: FREE R-VALUE / σ(F): 0
Details: LITTLE OF THE N-TERMINAL TAIL IS SEEN IN THE ELECTRON DENSITY MAP; SEGMENTS BUILT HERE VARY IN LENGTH AND CONFORMATION IN EACH SUBUNIT AND DO NOT OBEY THE NON-CRYSTALLOGRAPHIC SYMMETRY. FOR ...Details: LITTLE OF THE N-TERMINAL TAIL IS SEEN IN THE ELECTRON DENSITY MAP; SEGMENTS BUILT HERE VARY IN LENGTH AND CONFORMATION IN EACH SUBUNIT AND DO NOT OBEY THE NON-CRYSTALLOGRAPHIC SYMMETRY. FOR DETAILS OF THE RESIDUES RESTRAINED IN NCS GROUPS 1 AND 2, SEE JRNL REFERENCE. PARAMETER FILES FOR GLYCOLATE AND GLYCEROL ARE COMBINED INTO ONE FILE. TOPOLOGY FILES FOR GLYCOLATE AND GLYCEROL ARE COMBINED INTO ONE FILE.
RfactorNum. reflection% reflectionSelection details
Rfree0.294 4918 5 %RANDOM IN THIN SHELLS
Rwork0.247 ---
obs0.247 98864 85.3 %-
Refine analyzeLuzzati d res low obs: 25 Å / Luzzati sigma a obs: 0.57 Å
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31154 0 454 55 31663
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.54
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.14
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.17
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.451.5
X-RAY DIFFRACTIONx_mcangle_it5.242
X-RAY DIFFRACTIONx_scbond_it3.451.5
X-RAY DIFFRACTIONx_scangle_it5.242
Refine LS restraints NCSRms dev Biso : 3.21 Å2 / Rms dev position: 0.84 Å / Weight Biso : 1 / Weight position: 50
LS refinement shellResolution: 3→3.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 192 5 %
Rwork0.405 3769 -
obs--72 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3GLYCOLATE_GLYCEROL.PARGLYCOLATE_GLYCEROL.TOP
X-RAY DIFFRACTION4NADP.PARNADP.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.14
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17
LS refinement shell
*PLUS
Rfactor obs: 0.405

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