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- PDB-5fh2: The structure of rat cytosolic PEPCK variant E89Q in complex with GTP -

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Basic information

Entry
Database: PDB / ID: 5fh2
TitleThe structure of rat cytosolic PEPCK variant E89Q in complex with GTP
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / kinase / gluconeogenesis
Function / homology
Function and homology information


Gluconeogenesis / response to methionine / phosphoenolpyruvate carboxykinase activity / protein serine kinase activity (using GTP as donor) / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / cellular response to potassium ion starvation / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / glycerol biosynthetic process from pyruvate / propionate catabolic process ...Gluconeogenesis / response to methionine / phosphoenolpyruvate carboxykinase activity / protein serine kinase activity (using GTP as donor) / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / cellular response to potassium ion starvation / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / glycerol biosynthetic process from pyruvate / propionate catabolic process / cellular response to raffinose / tricarboxylic acid metabolic process / regulation of lipid biosynthetic process / response to interleukin-6 / cellular response to fructose stimulus / carboxylic acid binding / cellular hypotonic salinity response / cellular hypotonic response / cellular response to phorbol 13-acetate 12-myristate / oxaloacetate metabolic process / hepatocyte differentiation / positive regulation of memory T cell differentiation / cellular hyperosmotic response / glyceraldehyde-3-phosphate biosynthetic process / cellular hyperosmotic salinity response / nucleoside diphosphate kinase activity / response to lipid / response to starvation / cellular response to interleukin-1 / positive regulation of lipid biosynthetic process / cellular response to retinoic acid / cellular response to cAMP / cellular response to glucagon stimulus / cellular response to dexamethasone stimulus / response to activity / gluconeogenesis / response to insulin / response to bacterium / response to nutrient levels / cellular response to glucose stimulus / lipid metabolic process / cellular response to insulin stimulus / glucose metabolic process / GDP binding / glucose homeostasis / cellular response to tumor necrosis factor / peptidyl-serine phosphorylation / manganese ion binding / cellular response to hypoxia / response to lipopolysaccharide / GTP binding / magnesium ion binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / cytosol / cytoplasm
Similarity search - Function
Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 ...Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsJohnson, T.A. / Holyoak, T.
Funding support United States, Canada, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P20 RR17708 United States
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Biochemistry / Year: 2016
Title: Utilization of Substrate Intrinsic Binding Energy for Conformational Change and Catalytic Function in Phosphoenolpyruvate Carboxykinase.
Authors: Johnson, T.A. / Mcleod, M.J. / Holyoak, T.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3936
Polymers69,4991
Non-polymers8945
Water13,367742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-22 kcal/mol
Surface area24700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.717, 118.797, 60.528
Angle α, β, γ (deg.)90.000, 109.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoenolpyruvate carboxykinase, cytosolic [GTP] / PEPCK-C


Mass: 69498.680 Da / Num. of mol.: 1 / Mutation: E89Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Production host: Escherichia coli (E. coli)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 5 types, 747 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 742 / Source method: isolated from a natural source / Formula: H2O

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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: 2.18 Å3/Da / Density % sol: 43.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25% PEG 3350, 0.1M HEPES PH 7.4, 8MM MNCL2, 10mM GTP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.49→100 Å / Num. obs: 92558 / % possible obs: 96.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.08 / Χ2: 1.052 / Net I/av σ(I): 18.377 / Net I/σ(I): 21.3 / Num. measured all: 643595
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.49-1.534.70.30734211.1171.8
1.53-1.555.10.27138351.08879.4
1.55-1.585.40.24941061.09387.1
1.58-1.626.10.23245251.11394.4
1.62-1.6570.21948111.122100
1.65-1.697.10.20547851.105100
1.69-1.737.20.18648501.003100
1.73-1.787.20.1747541.02100
1.78-1.837.20.15547941.016100
1.83-1.897.30.14648141.041100
1.89-1.967.30.13748001.01699.9
1.96-2.047.30.12947551.04199.9
2.04-2.137.30.12247951.00199.9
2.13-2.247.40.11748011.02499.7
2.24-2.387.40.10447991.0499.9
2.38-2.567.40.0947701.02399.7
2.56-2.827.40.08548101.00999.7
2.82-3.237.30.08147861.0899.4
3.23-4.077.40.06448151.06899.6
4.07-1007.20.05447321.11596.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QEY

2qey


Resolution: 1.49→59.4 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.2127 / WRfactor Rwork: 0.1811 / FOM work R set: 0.8995 / SU B: 1.098 / SU ML: 0.042 / SU R Cruickshank DPI: 0.0668 / SU Rfree: 0.0674 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1723 4756 5.1 %RANDOM
Rwork0.1471 ---
obs0.1484 87764 95.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.04 Å2 / Biso mean: 24.877 Å2 / Biso min: 13.6 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.49→59.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4819 0 50 742 5611
Biso mean--20.25 36.85 -
Num. residues----613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195052
X-RAY DIFFRACTIONr_bond_other_d0.0020.024791
X-RAY DIFFRACTIONr_angle_refined_deg1.6381.9736860
X-RAY DIFFRACTIONr_angle_other_deg0.98311096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.355629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92824.311225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05215867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4961529
X-RAY DIFFRACTIONr_chiral_restr0.0960.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215681
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021132
X-RAY DIFFRACTIONr_mcbond_it1.6372.2142468
X-RAY DIFFRACTIONr_mcbond_other1.6372.2132467
X-RAY DIFFRACTIONr_mcangle_it2.453.3223086
LS refinement shellResolution: 1.491→1.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 255 -
Rwork0.232 4530 -
all-4785 -
obs--67.5 %

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