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- PDB-1hkb: CRYSTAL STRUCTURE OF RECOMBINANT HUMAN BRAIN HEXOKINASE TYPE I CO... -

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Database: PDB / ID: 1hkb
TitleCRYSTAL STRUCTURE OF RECOMBINANT HUMAN BRAIN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE AND GLUCOSE-6-PHOSPHATE
ComponentsD-GLUCOSE 6-PHOSPHOTRANSFERASE
KeywordsPHOSPHOTRANSFERASE / GLYCOLYSIS / ALLOSTERIC ENZYME / GLUCOSE / GLUCOSE-6-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 / 6-O-phosphono-alpha-D-glucopyranose / Hexokinase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAleshin, A.E. / Zeng, C. / Burenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
Citation
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.
#1: 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
DepositionDec 1, 1997Processing site: BNL
Revision 1.0Jun 3, 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: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn
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.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_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_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 1.4Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-GLUCOSE 6-PHOSPHOTRANSFERASE
B: D-GLUCOSE 6-PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,17214
Polymers205,2502
Non-polymers1,92112
Water2,558142
1
A: D-GLUCOSE 6-PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5867
Polymers102,6251
Non-polymers9616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-GLUCOSE 6-PHOSPHOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,5867
Polymers102,6251
Non-polymers9616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.000, 122.000, 123.000
Angle α, β, γ (deg.)90.00, 92.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.999648, -0.026325, -0.003239), (-0.022783, 0.914761, -0.403353), (0.013581, -0.403137, -0.915039)
Vector: 77.72993, 14.75741, 64.59476)

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Components

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


Mass: 102625.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CRYSTALLIZES AS A DIMER IN ASYMMETRIC UNIT / Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM / Organ: BRAIN / Plasmid: PET-11A / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / 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.: 4
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: Sugar
ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE COMPLEX OF BRAIN HEXOKINASE WITH GLC AND G6P CRYSTALLIZES AS A HOMODIMER. EACH SUBUNIT (CHAINS ...THE COMPLEX OF BRAIN HEXOKINASE WITH GLC AND G6P CRYSTALLIZES AS A HOMODIMER. EACH SUBUNIT (CHAINS A AND B) CONSISTS OF TWO STRUCTURALLY SIMILAR DOMAINS (50% SEQUENCE IDENTITY). THE DOMAINS ARE ALSO STRUCTURALLY HOMOLOGOUS TO YEAST HEXOKINASE (30% SEQUENCE IDENTITY). THE N-TERMINAL DOMAIN IS REGULATORY AND THE C-TERMINAL DOMAIN IS CATALYTIC. ALL DOMAINS OF ALL CHAINS CONTAIN BOUND SUBSTRATE GLUCOSE AND INHIBITOR GLUCOSE-6-PHOSPHATE. FAR FROM THE ACTIVE SITE THERE ARE ALSO 4 SITES OF BOUND SOLVENT WHICH ARE LIKELY TO BE METAL IONS.

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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: 3.03 Å3/Da / Density % sol: 52 %
Crystal growpH: 5.6
Details: HEXOKINASE WAS CRYSTALLIZED BY MIXING 20 MG/ML OF PROTEIN SOLUTION WITH 6% PEG 8000, 0.1 M NA CITRATE, PH 5.6, 0.1 M NA ACETATE, 20 MM GLUCOSE-6-PHOSPHATE, AND PRESUMABLE TRACE AMOUNT OF ...Details: HEXOKINASE WAS CRYSTALLIZED BY MIXING 20 MG/ML OF PROTEIN SOLUTION WITH 6% PEG 8000, 0.1 M NA CITRATE, PH 5.6, 0.1 M NA ACETATE, 20 MM GLUCOSE-6-PHOSPHATE, AND PRESUMABLE TRACE AMOUNT OF GLUCOSE LEFT AFTER PURIFICATION; THEN SOAKED WITH 10 MM G6P AND 5 MM GLUCOSE.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop was combined with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
220 mMGluc-6-P1drop
35-7 %(w/v)PEG80001reservoir
420 mMGluc-6-P1reservoir
50.1 Msodium acetate1reservoir
60.1 Msodium citrate1reservoir

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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: 2.79→38 Å / Num. obs: 113243 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 62.4 Å2 / Rsym value: 0.055 / Net I/σ(I): 13
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 3 / Rsym value: 0.32 / % possible all: 88
Reflection
*PLUS
Num. measured all: 58613 / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
% possible obs: 88 % / Rmerge(I) obs: 0.32

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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: YEAST HEXOKINASE COMPLEXED WITH GLUCOSE (BARTUNIK, UNPUBLISHED)

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
Details: TOPOLOGY AND ENERGY PARAMETERS FOR GLUCOSE-6-PHOSPHATE WERE BUILT BY ANALOGY TO THOSE OF GLUCOSE AND ARE PRESENTED IN FILES PAR.HK AND TOP.HK
RfactorNum. reflection% reflectionSelection details
Rfree0.27 5653 10.2 %RANDOM
Rwork0.2 ---
obs0.2 55607 96.4 %-
Displacement parametersBiso mean: 44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14066 0 116 142 14324
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.831.5
X-RAY DIFFRACTIONx_mcangle_it5.972
X-RAY DIFFRACTIONx_scbond_it6.072
X-RAY DIFFRACTIONx_scangle_it9.382.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.06 Å / Weight Biso : 4 / Weight position: 100

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)
11RESTRAINTS8.2
224.7
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 887 10.1 %
Rwork0.308 7856 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PAR.HKTOPH19.SOL
X-RAY DIFFRACTION3PARAM3.CHOTOP.HK
X-RAY DIFFRACTION4TOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.55
LS refinement shell
*PLUS
Rfactor obs: 0.308

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