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- PDB-4lc9: Structural Basis for Regulation of Human Glucokinase by Glucokina... -

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Basic information

Entry
Database: PDB / ID: 4lc9
TitleStructural Basis for Regulation of Human Glucokinase by Glucokinase Regulatory Protein
Components
  • Glucokinase regulatory protein
  • Glucokinase
KeywordsTRANSFERASE/TRANSFERASE REGULATOR / Type 2 Diabetes / TRANSFERASE-TRANSFERASE REGULATOR complex
Function / homology
Function and homology information


negative regulation of hexokinase activity / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / detection of glucose / negative regulation of glucokinase activity / fructose-6-phosphate binding / positive regulation of glucokinase activity / mannokinase activity / carbohydrate derivative metabolic process / regulation of potassium ion transport ...negative regulation of hexokinase activity / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective GCK causes maturity-onset diabetes of the young 2 (MODY2) / detection of glucose / negative regulation of glucokinase activity / fructose-6-phosphate binding / positive regulation of glucokinase activity / mannokinase activity / carbohydrate derivative metabolic process / regulation of potassium ion transport / urate metabolic process / hexokinase / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / response to fructose / 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 / enzyme inhibitor activity / cellular response to leptin stimulus / glucose binding / canonical glycolysis / regulation of glycolytic process / Glycolysis / triglyceride homeostasis / cellular glucose homeostasis / protein localization to nucleus / 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 / protein import into nucleus / glucose metabolic process / glucose homeostasis / carbohydrate binding / protein domain specific binding / enzyme binding / mitochondrion / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Glucokinase regulatory protein family signature. / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Hexokinase-4, chordate / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase domain profile. / Hexokinase / Hexokinase domain signature. / Hexokinase ...Glucokinase regulatory protein family signature. / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Hexokinase-4, chordate / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase domain profile. / Hexokinase / Hexokinase domain signature. / Hexokinase / Hexokinase / Hexokinase, binding site / Hexokinase, C-terminal / Hexokinase, N-terminal / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-fructofuranose / Hexokinase-4 / Glucokinase regulatory protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsBeck, T. / Miller, B.G.
CitationJournal: Biochemistry / Year: 2013
Title: Structural basis for regulation of human glucokinase by glucokinase regulatory protein.
Authors: Beck, T. / Miller, B.G.
History
DepositionJun 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jul 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _entity.pdbx_description / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucokinase regulatory protein
B: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,6404
Polymers123,3572
Non-polymers2832
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.663, 105.312, 132.406
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glucokinase regulatory protein / / Glucokinase regulator


Mass: 70152.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gckr / Production host: Escherichia coli (E. coli) / References: UniProt: Q07071
#2: Protein Glucokinase / / Hexokinase type IV / HK IV / Hexokinase-4 / HK4 / Hexokinase-D


Mass: 53204.465 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCK / Production host: Escherichia coli (E. coli) / References: UniProt: P35557, glucokinase
#3: Sugar ChemComp-F6P / 6-O-phosphono-beta-D-fructofuranose / Fructose 6-phosphate


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
b-D-Fruf6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na

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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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: Crystals were obtained at 20 C by mixing 200 nL of GCK-GKRP-F6P complex solution with 100 nL of reservoir solution containing 0.1 M HEPES, pH 7.1, and 8% w/v PEG 6000, VAPOR DIFFUSION, ...Details: Crystals were obtained at 20 C by mixing 200 nL of GCK-GKRP-F6P complex solution with 100 nL of reservoir solution containing 0.1 M HEPES, pH 7.1, and 8% w/v PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2012
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→48.93 Å / Num. all: 18995 / Num. obs: 18946 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.73 / Redundancy: 6.5 % / Rmerge(I) obs: 0.0712 / Net I/σ(I): 12.93
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 6.23 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 1.73 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→48.929 Å / SU ML: 0.57 / σ(F): 1.33 / Phase error: 34.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2922 976 5.15 %
Rwork0.2437 --
obs0.2461 18946 99.92 %
all-18995 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→48.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7682 0 17 0 7699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067817
X-RAY DIFFRACTIONf_angle_d0.95710542
X-RAY DIFFRACTIONf_dihedral_angle_d13.1862937
X-RAY DIFFRACTIONf_chiral_restr0.0381210
X-RAY DIFFRACTIONf_plane_restr0.0051353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.57920.40131470.34582475X-RAY DIFFRACTION100
3.5792-3.80340.4081390.29852533X-RAY DIFFRACTION100
3.8034-4.09690.37951360.2772518X-RAY DIFFRACTION100
4.0969-4.5090.27411550.23372536X-RAY DIFFRACTION100
4.509-5.16080.25791420.21682563X-RAY DIFFRACTION100
5.1608-6.49960.28361350.27442607X-RAY DIFFRACTION100
6.4996-48.93390.26781220.21982738X-RAY DIFFRACTION100

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