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- PDB-3w0l: The crystal structure of Xenopus Glucokinase and Glucokinase Regu... -

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Basic information

Entry
Database: PDB / ID: 3w0l
TitleThe crystal structure of Xenopus Glucokinase and Glucokinase Regulatory Protein complex
Components
  • Glucokinase regulatory protein
  • Glucokinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / aba sandwich / typical hexokanse fold / kinase / sugar binding / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


detection of glucose / hexose metabolic process / negative regulation of glucokinase activity / fructose-6-phosphate binding / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / carbohydrate derivative metabolic process / glucokinase activity / glucose binding / intracellular glucose homeostasis / positive regulation of glycogen biosynthetic process ...detection of glucose / hexose metabolic process / negative regulation of glucokinase activity / fructose-6-phosphate binding / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / carbohydrate derivative metabolic process / glucokinase activity / glucose binding / intracellular glucose homeostasis / positive regulation of glycogen biosynthetic process / negative regulation of gluconeogenesis / glycolytic process / positive regulation of insulin secretion / glucose homeostasis / carbohydrate metabolic process / mitochondrion / nucleoplasm / ATP binding / cytoplasm
Similarity search - Function
Rossmann fold - #12620 / Hexokinase-4, chordate / Helicase, Ruva Protein; domain 3 - #1080 / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Glucokinase regulatory protein family signature. / Hexokinase; domain 1 / Hexokinase; domain 1 - #20 / Hexokinase / Hexokinase, binding site ...Rossmann fold - #12620 / Hexokinase-4, chordate / Helicase, Ruva Protein; domain 3 - #1080 / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Glucokinase regulatory protein family signature. / 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. / SIS domain / SIS domain profile. / Glucose-6-phosphate isomerase like protein; domain 1 / ATPase, nucleotide binding domain / Helicase, Ruva Protein; domain 3 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FRUCTOSE -6-PHOSPHATE / Phosphotransferase / Glucokinase regulatory protein
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.92 Å
AuthorsChoi, J.M. / Seo, M.H. / Kyeong, H.H. / Kim, E. / Kim, H.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Molecular basis for the role of glucokinase regulatory protein as the allosteric switch for glucokinase
Authors: Choi, J.M. / Seo, M.H. / Kyeong, H.H. / Kim, E. / Kim, H.S.
History
DepositionOct 31, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)240,86612
Polymers239,9154
Non-polymers9518
Water1,53185
1
A: Glucokinase
B: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5297
Polymers119,9582
Non-polymers5715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-73 kcal/mol
Surface area40440 Å2
MethodPISA
2
C: Glucokinase
D: Glucokinase regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,3375
Polymers119,9582
Non-polymers3793
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-37 kcal/mol
Surface area39190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.318, 130.030, 175.117
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Glucokinase / / Hexokinase IV


Mass: 51144.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: gck / Production host: Escherichia coli (E. coli) / References: UniProt: Q91753, glucokinase
#2: Protein Glucokinase regulatory protein / / Hexokinase IV inhibitor / Glucokinase regulator


Mass: 68813.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: gckr / Production host: Escherichia coli (E. coli) / References: UniProt: Q91754

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Non-polymers , 4 types, 93 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-F6R / FRUCTOSE -6-PHOSPHATE / Fructose 6-phosphate


Mass: 260.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O9P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS SEUQENCE IS ACCORDING TO REFERENCE SEQUENCE NM_001089807.

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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: 2.59 Å3/Da / Density % sol: 52.58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.005M MgSO4, 0.05M MES, 5% PEG4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Oct 22, 2011 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 54529 / Num. obs: 54157 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 50.23 Å2
Reflection shellResolution: 2.9→2.95 Å / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V4T, 1NRI

1v4t

1nri


Resolution: 2.92→28.478 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.5 / σ(F): 1.33 / Phase error: 28.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2772 2662 4.99 %random
Rwork0.242 ---
all0.247 53375 --
obs0.2438 53354 97.32 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.667 Å2 / ksol: 0.299 e/Å3
Displacement parametersBiso max: 139.34 Å2 / Biso mean: 54.8746 Å2 / Biso min: 15.78 Å2
Baniso -1Baniso -2Baniso -3
1--20.2106 Å20 Å20 Å2
2--18.1073 Å20 Å2
3---2.1033 Å2
Refinement stepCycle: LAST / Resolution: 2.92→28.478 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15661 0 54 85 15800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315963
X-RAY DIFFRACTIONf_angle_d0.53121537
X-RAY DIFFRACTIONf_chiral_restr0.0372466
X-RAY DIFFRACTIONf_plane_restr0.0022755
X-RAY DIFFRACTIONf_dihedral_angle_d13.4595947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9203-2.97330.54361110.48852207231881
2.9733-3.03040.57911370.45112599273696
3.0304-3.09220.46471360.39032590272696
3.0922-3.15940.44291390.33812629276898
3.1594-3.23280.34511420.27562690283299
3.2328-3.31350.31631430.260627122855100
3.3135-3.40290.2851420.273327042846100
3.4029-3.50290.29451430.272227162859100
3.5029-3.61580.28211440.272327202864100
3.6158-3.74470.31761420.260727072849100
3.7447-3.89430.25841430.21222705284899
3.8943-4.0710.2451410.21682645278696
4.071-4.2850.25181340.21292601273595
4.285-4.55250.22771420.19062715285799
4.5525-4.90230.26361370.19882669280697
4.9023-5.39270.22821460.21442722286899
5.3927-6.16610.27591460.245827672913100
6.1661-7.74270.22921480.207128172965100
7.7427-28.4790.18191460.18382777292395

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