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- PDB-1dgk: MUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I WITH GLUCOS... -

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Basic information

Entry
Database: PDB / ID: 1dgk
TitleMUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I WITH GLUCOSE AND ADP IN THE ACTIVE SITE
ComponentsHEXOKINASE TYPE I
KeywordsTRANSFERASE / BRAIN HEXOKINASE / MAMMALIAN HEXOKINASE 1 / SUGAR KINASE
Function / homology
Function and homology information


Defective HK1 causes hexokinase deficiency (HK deficiency) / glucosamine kinase activity / GDP-mannose biosynthetic process from mannose / hexokinase activity / Synthesis of GDP-mannose / carbohydrate phosphorylation / maintenance of protein location in mitochondrion / mannokinase activity / hexokinase / establishment of protein localization to mitochondrion ...Defective HK1 causes hexokinase deficiency (HK deficiency) / glucosamine kinase activity / GDP-mannose biosynthetic process from mannose / hexokinase activity / Synthesis of GDP-mannose / carbohydrate phosphorylation / maintenance of protein location in mitochondrion / mannokinase activity / hexokinase / establishment of protein localization to mitochondrion / GDP-mannose biosynthetic process / fructokinase activity / glucokinase activity / mannose metabolic process / positive regulation of cytokine production involved in immune response / glucose 6-phosphate metabolic process / peptidoglycan binding / D-glucose binding / fructose 6-phosphate metabolic process / canonical glycolysis / Glycolysis / intracellular glucose homeostasis / positive regulation of interleukin-1 beta production / glycolytic process / glucose metabolic process / mitochondrial outer membrane / membrane raft / inflammatory response / innate immune response / mitochondrion / 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
ADENOSINE-5'-DIPHOSPHATE / alpha-D-glucopyranose / PHOSPHATE ION / Hexokinase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsAleshin, A.E. / Liu, X. / Kirby, C. / Bourenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of mutant monomeric hexokinase I reveal multiple ADP binding sites and conformational changes relevant to allosteric regulation.
Authors: Aleshin, A.E. / Kirby, C. / Liu, X. / Bourenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
#1: Journal: J.Mol.Biol. / Year: 1998
Title: Regulation of Hexokinase I: Crystal Structure of Recombinant Human Brain Hexokinase Complexed with Glucose and Phosphate
Authors: Aleshin, A.E. / Zeng, C. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
#2: Journal: Structure / Year: 1998
Title: The Mechanism of Regulation of Hexokinase: New Insights from the Crystal Structure of Recombinant Human Brain Hexokinase Complexed with Glucose and Glucose-6-Phosphate
Authors: Aleshin, A.E. / Zeng, C. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
History
DepositionNov 24, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Jul 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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 3, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: HEXOKINASE TYPE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8676
Polymers102,5571
Non-polymers1,3105
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.780, 146.830, 58.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HEXOKINASE TYPE I / HK I / BRAIN FORM HEXOKINASE


Mass: 102556.984 Da / Num. of mol.: 1 / Mutation: E280A, R283A, G284Y, T536A
Source method: isolated from a genetically manipulated source
Details: SECOND MOLECULE OF ADP IS BOUND NEAR THE N-TERMINUS OF THE POLYPEPTIDE CHAIN. THE REGULATORY SITE OF THE N-TERMINAL DOMAIN IS OCCUPIED WITH GLUCOSE AND PHOSPHATE. MUTATIONS IN DIMER INTERFACE AND THE ACTIVE SITE
Source: (gene. exp.) Homo sapiens (human) / Cell: NEURON / Organ: BRAIN / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: P19367, hexokinase
#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.: 2 / Source method: obtained synthetically / 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, SODIUM ACETATE, MES, ADP, GLUCOSE, GLUCOSE-6-PHOSPHATE. GROWN CRYSTALS WERE SOAKED WITH THE SAME BUFFER, BUT W/O GLUCOSE-6-PHOSPHATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and precipitant solutions
PH range low: 6.5 / PH range high: 5.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
214-18 %(w/v)PEG80001reservoirprecipitant
3200 mMMES1reservoirprecipitant
4200 mMsodium acetate1reservoirprecipitant
520 mMADP1reservoirprecipitant
62 mM1reservoirprecipitantAl(NO3)3
710 mM1reservoirprecipitantNaF
830 mMmagnesium acetate1reservoirprecipitant

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→50 Å / Num. all: 65575 / Num. obs: 25465 / % possible obs: 78 % / Redundancy: 2.64 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15
Reflection shellResolution: 2.77→2.98 Å / Redundancy: 2 % / Rmerge(I) obs: 0.46 / % possible all: 57
Reflection
*PLUS
Num. obs: 25491 / % possible obs: 77.5 % / Num. measured all: 65575
Reflection shell
*PLUS
% possible obs: 57 % / Rmerge(I) obs: 0.44

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: USED MAXIMUM LIKELIHOOD RESIDUALS AND CONJUGATE DIRECTION MINIMIZATION.SIDE CHAINS OF RESIDUES 16, 17, 20, 21, 24, 101, 102, 252, 353, 794-799, 801, 804, 806, 809-811 HAVE POOR ELECTRON ...Details: USED MAXIMUM LIKELIHOOD RESIDUALS AND CONJUGATE DIRECTION MINIMIZATION.SIDE CHAINS OF RESIDUES 16, 17, 20, 21, 24, 101, 102, 252, 353, 794-799, 801, 804, 806, 809-811 HAVE POOR ELECTRON DENSITY. THEIR OCCUPANCIES ARE SET TO 0.01
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1241 -RANDOM
Rwork0.258 ---
all0.26 23882 --
obs0.26 23882 78 %-
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7079 0 83 94 7256
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d0.039
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.31 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.04

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