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- PDB-1v4t: Crystal structure of human glucokinase -

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Basic information

Entry
Database: PDB / ID: 1v4t
TitleCrystal structure of human glucokinase
Componentsglucokinase isoform 2
KeywordsTRANSFERASE / hexokinase IV / allosteric enzyme / diabetes
Function / homology
Function and homology information


Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / detection of glucose / mannokinase activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / NADP metabolic process ...Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / detection of glucose / mannokinase activity / regulation of potassium ion transport / hexokinase / fructokinase activity / carbohydrate phosphorylation / 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) / calcium ion import / cellular response to leptin stimulus / glucose binding / canonical glycolysis / regulation of glycolytic process / Glycolysis / cellular glucose homeostasis / Regulation of gene expression in beta cells / regulation of insulin secretion / positive regulation of insulin secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / glycolytic process / cellular response to insulin stimulus / glucose metabolic process / glucose homeostasis / mitochondrion / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Hexokinase-4, chordate / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. ...Hexokinase-4, chordate / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsKamata, K. / Mitsuya, M. / Nishimura, T. / Eiki, J. / Nagata, Y.
CitationJournal: Structure / Year: 2004
Title: Structural basis for allosteric regulation of the monomeric allosteric enzyme human glucokinase
Authors: Kamata, K. / Mitsuya, M. / Nishimura, T. / Eiki, J. / Nagata, Y.
History
DepositionNov 19, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: glucokinase isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8264
Polymers50,6111
Non-polymers2153
Water1267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.180, 103.180, 281.020
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein glucokinase isoform 2


Mass: 50610.500 Da / Num. of mol.: 1 / Fragment: RESIDUES 15-465
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pFLAG-CTC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5A / References: UniProt: P35557, hexokinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 4.61 Å3/Da / Density % sol: 73.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: Ammonium sulfate, Bicine, Sodium chloride, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 9, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→87.71 Å / Num. obs: 12925 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 77.8 Å2 / Rsym value: 0.088 / Net I/σ(I): 6.84
Reflection shellResolution: 3.4→3.58 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.214 / % possible all: 100

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Processing

Software
NameVersionClassification
CNX2002refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V4S
Resolution: 3.4→48.43 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2102820.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1292 10.4 %RANDOM
Rwork0.237 ---
all0.256 12918 --
obs0.244 12463 96.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 14.7978 Å2 / ksol: 0.337635 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-10.33 Å230.59 Å20 Å2
2--10.33 Å20 Å2
3----20.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.58 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 3.4→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 11 7 3343
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_angle_deg1.2
X-RAY DIFFRACTIONo_dihedral_angle_d22.1
X-RAY DIFFRACTIONo_improper_angle_d0.76
X-RAY DIFFRACTIONo_mcbond_it1.971.5
X-RAY DIFFRACTIONo_mcangle_it3.472
X-RAY DIFFRACTIONo_scbond_it2.772
X-RAY DIFFRACTIONo_scangle_it4.582.5
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.377 213 10.8 %
Rwork0.306 1766 -
obs-1979 95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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