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- PDB-3qic: The structure of human glucokinase E339K mutation -

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Basic information

Entry
Database: PDB / ID: 3qic
TitleThe structure of human glucokinase E339K mutation
ComponentsGlucokinase
KeywordsTRANSFERASE / Glycolysis / Kinase / Sugar Binding / Phosphorylation
Function / homology
Function and homology information


Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / glucose sensor activity / mannokinase activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucose catabolic process / glucokinase activity / glucose 6-phosphate metabolic process ...Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / glucose sensor activity / mannokinase activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucose catabolic process / glucokinase activity / glucose 6-phosphate metabolic process / NADP metabolic process / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / D-glucose binding / cellular response to leptin stimulus / canonical glycolysis / calcium ion import / Glycolysis / regulation of glycolytic process / intracellular glucose homeostasis / Regulation of gene expression in beta cells / positive regulation of glycogen biosynthetic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / response to glucose / regulation of insulin secretion / glycolytic process / positive regulation of insulin secretion / cellular response to insulin stimulus / glucose metabolic process / glucose homeostasis / mitochondrion / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. ...Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-glucopyranose / Hexokinase-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiu, Q. / Liu, S. / Liu, J.
CitationJournal: Febs Lett. / Year: 2011
Title: Crystal structure of E339K mutated human glucokinase reveals changes in the ATP binding site.
Authors: Liu, Q. / Shen, Y. / Liu, S. / Weng, J. / Liu, J.
History
DepositionJan 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 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 1.5Oct 30, 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: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8098
Polymers53,0761
Non-polymers7337
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.740, 80.740, 178.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glucokinase / Hexokinase type IV / HK IV / Hexokinase-4 / HK4 / Hexokinase-D


Mass: 53076.230 Da / Num. of mol.: 1 / Fragment: residues 12-465 / Mutation: E339K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCK / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 / References: UniProt: P35557, glucokinase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 25% (w/v) PEG3350, 0.1M HEPES pH 7.3, 0.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorType: RAYONIX MX-225 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→41.19 Å / Num. obs: 30831 / % possible obs: 99.9 % / Observed criterion σ(I): 1 / Redundancy: 6 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.077
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.2-2.326.10.5443.4266651100
6.96-41.195.10.02927.25504196.3

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V4S

1v4s


Resolution: 2.2→39.375 Å / SU ML: 0.29 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2502 1523 5.05 %
Rwork0.2126 --
obs0.2145 30165 97.91 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.626 Å2 / ksol: 0.385 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.149 Å20 Å2-0 Å2
2--0.149 Å20 Å2
3----0.298 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3563 0 48 51 3662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083660
X-RAY DIFFRACTIONf_angle_d1.0854906
X-RAY DIFFRACTIONf_dihedral_angle_d15.3321394
X-RAY DIFFRACTIONf_chiral_restr0.068535
X-RAY DIFFRACTIONf_plane_restr0.004635
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.27860.32171420.2673267994
2.2786-2.36980.33841480.2604273495
2.3698-2.47770.29661710.2421275797
2.4777-2.60830.26221340.2239280497
2.6083-2.77170.29571510.2338285299
2.7717-2.98560.31021480.2436288699
2.9856-3.28590.26871660.22692882100
3.2859-3.76110.2331610.2012936100
3.7611-4.73730.20551540.17462988100
4.7373-39.38090.22981480.2123312498

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