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- PDB-1cza: MUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I COMPLEXED W... -

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Entry
Database: PDB / ID: 1cza
TitleMUTANT MONOMER OF RECOMBINANT HUMAN HEXOKINASE TYPE I COMPLEXED WITH GLUCOSE, GLUCOSE-6-PHOSPHATE, AND ADP
ComponentsHEXOKINASE TYPE I
KeywordsTRANSFERASE / STRUCTURALLY HOMOLOGOUS DOMAINS
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 / 6-O-phosphono-alpha-D-glucopyranose / alpha-D-glucopyranose / Hexokinase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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. / Bourenkov, G.P. / Bartunik, H.D. / Fromm, H.J. / Honzatko, R.B.
History
DepositionSep 1, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 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 1.5Feb 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)103,8956
Polymers102,5871
Non-polymers1,3085
Water12,106672
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.660, 145.800, 58.130
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


Mass: 102587.008 Da / Num. of mol.: 1 / Mutation: E280A, R283A, G284Y
Source method: isolated from a genetically manipulated source
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: 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.: 2 / Source method: obtained synthetically / Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 672 / Source method: isolated from a natural source / Formula: H2O
Compound detailsWILD-TYPE HEXOKINASE I IS A MONOMER AT CONCENTRATION BELOW 1 MG/ML. THE MUTANT IN THIS ENTRY IS A ...WILD-TYPE HEXOKINASE I IS A MONOMER AT CONCENTRATION BELOW 1 MG/ML. THE MUTANT IN THIS ENTRY IS A MONOMER AT CONCENTRATION UP TO 15 MG/ML.

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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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: PEG 8000, SODIUM ACETATE, MES, ADP, ALUMINUM NITRATE, SODIUM FLUORIDE, MAGNESIUM ACETATE, GLUCOSE, pH 6.5, EVAPORATION, temperature 298.0K
Crystal grow
*PLUS
pH: 7.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein11
214-18 %PEG800012
3100 mMMES12
4150-250 mMsodium acetate12
520 mMADP12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.9→17 Å / Num. all: 96631 / Num. obs: 96631 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.55 / % possible all: 98.3
Reflection
*PLUS
Num. obs: 83349 / % possible obs: 98.6 % / Num. measured all: 286697 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 82.3 % / Rmerge(I) obs: 0.41

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→8 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
Details: USED MAXIMUM LIKELIHOOD RESIDUALS AND CONJUGATE DIRECTION MINIMIZATION ADP is bound near the N-terminus of the polypeptide chain. Side chains of residues 16, 20, 24, 101, 102, 353, 794, 801, ...Details: USED MAXIMUM LIKELIHOOD RESIDUALS AND CONJUGATE DIRECTION MINIMIZATION ADP is bound near the N-terminus of the polypeptide chain. Side chains of residues 16, 20, 24, 101, 102, 353, 794, 801, 811 have poor electron density. Their occupancies are set to 0.01.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 4769 -RANDOM
Rwork0.211 ---
all0.213 95270 --
obs0.213 95270 100 %-
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7097 0 83 679 7859
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.033
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
Highest resolution: 2 Å / Rfactor Rfree: 0.268
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0360.04

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