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- PDB-2bhl: X-RAY STRUCTURE OF HUMAN GLUCOSE-6-PHOSPHATE DEHYDROGENASE (DELET... -

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Basic information

Entry
Database: PDB / ID: 2bhl
TitleX-RAY STRUCTURE OF HUMAN GLUCOSE-6-PHOSPHATE DEHYDROGENASE (DELETION VARIANT) COMPLEXED WITH GLUCOSE-6-PHOSPHATE
ComponentsGLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
KeywordsOXIDOREDUCTASE / OXIDOREDUCTASE (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 / cytoplasmic side of plasma membrane / centriolar satellite / 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 / 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 / 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: 2.9 Å
AuthorsKotaka, M. / Gover, S. / Lam, V.M.S. / Adams, M.J.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structural Studies of Glucose-6-Phosphate and Nadp+ Binding to Human Glucose-6-Phosphate Dehydrogenase
Authors: Kotaka, M. / Gover, S. / Vandeputte-Rutten, L. / Au, S.W.N. / Lam, V.M.S. / Adams, M.J.
#1: 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.
#2: 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
DepositionJan 13, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2005Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Other / Refinement description ...Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 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
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 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

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)113,86710
Polymers112,7952
Non-polymers1,0738
Water1,45981
1
A: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
B: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules

A: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
B: GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,73520
Polymers225,5894
Non-polymers2,14616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
MethodPQS
Unit cell
Length a, b, c (Å)117.552, 179.527, 137.938
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99911, -0.00678, -0.04166), (-0.03191, -0.52464, 0.85073), (-0.02763, 0.8513, 0.52395)
Vector: 35.44, 138.261, -76.298)

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Components

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


Mass: 56397.258 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THE 25 N-TERMINAL RESIDUES HAVE BEEN REMOVED AND THE FIRST RESIDUE IS VALINE, NOT HISTIDINE
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PTRC99A/DG6PD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DF213
References: UniProt: P11413, glucose-6-phosphate dehydrogenase (NADP+)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 59.8 %
Crystal growpH: 8.5
Details: 0.1M TRIS, PH 8.5; 0.2M MGCL2; 12% PEG 4000; 5% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 27, 2002 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.9→69 Å / Num. obs: 32261 / % possible obs: 98.9 % / Observed criterion σ(I): -4 / Redundancy: 6.8 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.3
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 92.9

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Processing

Software
NameVersionClassification
TNTBUSTER/TNTrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QKI CHAIN A, B

1qki


Resolution: 2.9→69 Å / Cross valid method: FREE R-VALUE / σ(F): 0
Details: RESIDUES 506 TO 515 WERE DISORDERED AND NOT INCLUDED
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1640 5 %RANDOM
Rwork0.212 ---
obs0.214 32261 98.9 %-
Refinement stepCycle: LAST / Resolution: 2.9→69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7754 0 68 81 7903
Refine LS restraints
Refine-IDTypeNumber
X-RAY DIFFRACTIONt_bond_d
X-RAY DIFFRACTIONt_angle_deg
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct994
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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