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- PDB-3moe: The structure of rat cytosolic PEPCK mutant A467G in complex with... -

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Entry
Database: PDB / ID: 3moe
TitleThe structure of rat cytosolic PEPCK mutant A467G in complex with Beta-Sulfopyruvate and GTP
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / kinase / gluconeogenesis
Function / homology
Function and homology information


Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process ...Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / cellular response to raffinose / tricarboxylic acid metabolic process / regulation of lipid biosynthetic process / response to interleukin-6 / cellular hypotonic response / cellular response to fructose stimulus / cellular hypotonic salinity response / glyceraldehyde-3-phosphate biosynthetic process / carboxylic acid binding / cellular response to phorbol 13-acetate 12-myristate / oxaloacetate metabolic process / hepatocyte differentiation / cellular hyperosmotic response / positive regulation of memory T cell differentiation / nucleoside diphosphate kinase activity / cellular hyperosmotic salinity response / response to lipid / response to starvation / cellular response to glucagon stimulus / positive regulation of lipid biosynthetic process / cellular response to interleukin-1 / cellular response to retinoic acid / cellular response to cAMP / cellular response to dexamethasone stimulus / response to nutrient levels / response to activity / gluconeogenesis / cellular response to glucose stimulus / response to bacterium / response to insulin / lipid metabolic process / cellular response to insulin stimulus / GDP binding / glucose metabolic process / glucose homeostasis / cellular response to tumor necrosis factor / manganese ion binding / cellular response to hypoxia / peptidyl-serine phosphorylation / response to lipopolysaccharide / GTP binding / magnesium ion binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / 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 / : / SULFOPYRUVATE / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsJohnson, T.A. / Holyoak, T.
CitationJournal: Biochemistry / Year: 2010
Title: Increasing the conformational entropy of the Omega-loop lid domain in phosphoenolpyruvate carboxykinase impairs catalysis and decreases catalytic fidelity .
Authors: Johnson, T.A. / Holyoak, T.
History
DepositionApr 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_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_asym_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 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
A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,41713
Polymers69,6301
Non-polymers1,78712
Water11,169620
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.324, 119.117, 60.053
Angle α, β, γ (deg.)90.000, 111.190, 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 / Phosphoenolpyruvate carboxylase


Mass: 69629.758 Da / Num. of mol.: 1 / Mutation: A467G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Plasmid: PGEX4T2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 7 types, 632 molecules

#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-SPV / SULFOPYRUVATE


Mass: 168.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O6S
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 298 K / Method: hanging drop vapor diffusion / pH: 7.4
Details: 12-30% PEG 3350, 0.1M HEPES PH 7.4,10 MM MNCL2, 10 MM GTP, hanging drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 9, 2009
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.25→100 Å / Num. obs: 152044 / % possible obs: 95 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.056 / Χ2: 1.045 / Net I/σ(I): 14.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.25-1.293.50.534107441.064167.2
1.29-1.354.70.468137101.056185.8
1.35-1.416.40.402155741.032197.7
1.41-1.487.10.316159771.0951100
1.48-1.577.50.219159571.061100
1.57-1.77.60.157160151.0751100
1.7-1.877.60.108159861.0621100
1.87-2.147.70.074159911.0341100
2.14-2.697.70.057160360.9411100
2.69-1007.60.035160541.057199.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-IceIcedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→20.57 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.188 / WRfactor Rwork: 0.16 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.889 / SU B: 1.378 / SU ML: 0.03 / SU R Cruickshank DPI: 0.042 / SU Rfree: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.174 7657 5 %RANDOM
Rwork0.148 ---
obs0.149 151977 94.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 62.54 Å2 / Biso mean: 11.025 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20.05 Å2
2---0.06 Å2-0 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.25→20.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4851 0 87 620 5558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0225292
X-RAY DIFFRACTIONr_angle_refined_deg2.5771.9787199
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8585679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51424.017239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80315922
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0221535
X-RAY DIFFRACTIONr_chiral_restr0.1680.2750
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0214060
X-RAY DIFFRACTIONr_mcbond_it1.4571.53180
X-RAY DIFFRACTIONr_mcangle_it2.36525160
X-RAY DIFFRACTIONr_scbond_it3.52132112
X-RAY DIFFRACTIONr_scangle_it5.574.52008
LS refinement shellResolution: 1.25→1.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 361 -
Rwork0.327 7065 -
all-7426 -
obs--63.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1176-0.0183-0.09420.69920.18920.9412-0.0140.0672-0.0365-0.0502-0.01730.00080.0369-0.01340.03130.0985-0.0127-0.00670.1361-0.02240.0964-1.138-18.693-7.997
20.27090.21120.04470.87360.30660.3056-0.01860.0634-0.0435-0.04720.0276-0.09-0.02740.0424-0.0090.0766-0.0108-0.0070.1224-0.01170.04484.998-5.945-5.109
30.5448-0.1066-0.06390.40220.12590.3476-0.02060.037-0.04140.03430.01390.03850.0575-0.0540.00680.0688-0.0191-0.01050.0834-0.00630.0309-8.196-2.83710.348
40.30530.1273-0.01140.61620.19890.3259-0.01660.0089-0.01370.03930.0113-0.01420.0362-0.01410.00530.0537-0.0065-0.01210.08090.00530.022-2.1654.27813.282
50.62470.2354-0.09640.6566-0.03640.38290.0125-0.07080.07950.07-0.02450.0461-0.0389-0.0070.01190.08780.0024-0.0230.0975-0.00940.0453-3.42418.15521.984
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 91
2X-RAY DIFFRACTION2A92 - 223
3X-RAY DIFFRACTION3A224 - 386
4X-RAY DIFFRACTION4A387 - 500
5X-RAY DIFFRACTION5A501 - 622

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