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- PDB-1hkc: RECOMBINANT HUMAN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE AND PH... -

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Basic information

Entry
Database: PDB / ID: 1hkc
TitleRECOMBINANT HUMAN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE AND PHOSPHATE
ComponentsD-GLUCOSE 6-PHOSPHOTRANSFERASE
KeywordsPHOSPHOTRANSFERASE / GLYCOLYSIS / ALLOSTERIC ENZYME / GLUCOSE / PHOSPHATE
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
beta-D-glucopyranose / : / PHOSPHATE ION / Hexokinase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAleshin, A.E. / Honzatko, R.B.
Citation
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.
#1: 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. / Bourenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
#2: Journal: FEBS Lett. / Year: 1996
Title: Crystallization and Preliminary X-Ray Analysis of Human Brain Hexokinase
Authors: Aleshin, A.E. / Zeng, C. / Fromm, H.J. / Honzatko, R.B.
History
DepositionJul 1, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5May 22, 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
A: D-GLUCOSE 6-PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0726
Polymers102,6241
Non-polymers4485
Water2,702150
1
A: D-GLUCOSE 6-PHOSPHOTRANSFERASE
hetero molecules

A: D-GLUCOSE 6-PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,14512
Polymers205,2482
Non-polymers89710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Unit cell
Length a, b, c (Å)175.090, 175.090, 99.470
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein D-GLUCOSE 6-PHOSPHOTRANSFERASE / HEXOKINASE I / HEXOKINASE TYPE I / HUMAN BRAIN HEXOKINASE


Mass: 102624.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM SURFACE OF MITOCHONDRIA / Organ: BRAIN / Plasmid: PET-11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19367, hexokinase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-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.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIN THIS STRUCTURE THE N-TERMINAL, REGULATORY DOMAIN IS IN THE CLOSED CONFORMATION AND CONTAINS ...IN THIS STRUCTURE THE N-TERMINAL, REGULATORY DOMAIN IS IN THE CLOSED CONFORMATION AND CONTAINS TIGHTLY BOUND GLUCOSE AND PHOSPHATE. THE C-TERMINAL, CATALYTIC DOMAIN IS OPEN AND ONLY CONTAINS LOOSELY BOUND PHOSPHATE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 70 %
Crystal growpH: 6.5
Details: HEXOKINASE WAS CRYSTALLIZED BY HANGING DROP METHOD AT ROOM TEMPERATURE BY MIXING 20 MG/ ML OF PROTEIN IN 25 MM POTASSIUM PHOSPHATE WITH A PRECIPITANT SOLUTION CONTAINING 5% PEG 8000 AND 0.1 ...Details: HEXOKINASE WAS CRYSTALLIZED BY HANGING DROP METHOD AT ROOM TEMPERATURE BY MIXING 20 MG/ ML OF PROTEIN IN 25 MM POTASSIUM PHOSPHATE WITH A PRECIPITANT SOLUTION CONTAINING 5% PEG 8000 AND 0.1 M NA CACODYLATE, PH 6.5. PROTEIN SAMPLES CONTAINED A TRACE AMOUNT OF GLUCOSE LEFT AFTER PURIFICATION.
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
25-7 %(w/v)PEG80001reservoir
30.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.8→99 Å / Num. obs: 42845 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 51.7 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.9 / % possible all: 95.7
Reflection
*PLUS
Num. measured all: 251876
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

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

1hkb


Resolution: 2.8→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.241 4128 10.2 %RANDOM
Rwork0.174 ---
obs0.174 40612 97.8 %-
Displacement parametersBiso mean: 33 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7033 0 24 150 7207
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.57
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.491.5
X-RAY DIFFRACTIONx_mcangle_it5.392
X-RAY DIFFRACTIONx_scbond_it5.92
X-RAY DIFFRACTIONx_scangle_it9.252.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.328 676 10.2 %
Rwork0.25 5941 -
obs--96.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PAR.HKTOPH19.SOL
X-RAY DIFFRACTION3TOP.HK
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_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.57
LS refinement shell
*PLUS
Rfactor Rwork: 0.25

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