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

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Basic information

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


Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / 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 / cellular response to potassium ion starvation / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process ...Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / 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 / cellular response to potassium ion starvation / 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 response to fructose stimulus / cellular hypotonic response / carboxylic acid binding / cellular hypotonic salinity response / cellular response to phorbol 13-acetate 12-myristate / glyceraldehyde-3-phosphate biosynthetic process / oxaloacetate metabolic process / hepatocyte differentiation / positive regulation of memory T cell differentiation / cellular hyperosmotic response / nucleoside diphosphate kinase activity / cellular hyperosmotic salinity response / 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 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 / glucose metabolic process / GDP binding / cellular response to tumor necrosis factor / glucose homeostasis / 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 / : / OXALATE ION / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)141,83521
Polymers139,2602
Non-polymers2,57519
Water16,448913
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A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,03711
Polymers69,6301
Non-polymers1,40710
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,79810
Polymers69,6301
Non-polymers1,1699
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.983, 119.601, 87.068
Angle α, β, γ (deg.)90.000, 106.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 69629.758 Da / Num. of mol.: 2 / 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, 932 molecules

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


Mass: 523.180 Da / Num. of mol.: 2 / 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.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2O4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


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


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 913 / 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: 2.22 Å3/Da / Density % sol: 44.54 %
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: 1.75→100 Å / Num. obs: 118295 / % possible obs: 96.7 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.094 / Χ2: 1.06 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.816.90.74115531.099194.9
1.81-1.896.90.552115881.082195.1
1.89-1.9770.414115581.082194.9
1.97-2.0770.273116161.092194.9
2.07-2.27.10.199116911.037196
2.2-2.387.10.154118550.994197.1
2.38-2.617.20.124119711.088198
2.61-2.997.40.091120990.998198.8
2.99-3.777.40.061121421.015198.9
3.77-1007.20.047122221.121198.6

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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: 1.75→33.24 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.805 / SU B: 6.527 / SU ML: 0.096 / SU R Cruickshank DPI: 0.13 / SU Rfree: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.228 5926 5 %RANDOM
Rwork0.179 ---
obs0.182 118250 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 59.23 Å2 / Biso mean: 11.414 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20.18 Å2
2---0.23 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9733 0 146 913 10792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02210393
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.97814122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.26451307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96224.307462
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.481151776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9051559
X-RAY DIFFRACTIONr_chiral_restr0.1040.21472
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217944
X-RAY DIFFRACTIONr_mcbond_it0.7961.56280
X-RAY DIFFRACTIONr_mcangle_it1.349210156
X-RAY DIFFRACTIONr_scbond_it2.24934113
X-RAY DIFFRACTIONr_scangle_it3.5134.53931
LS refinement shellResolution: 1.75→1.793 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 427 -
Rwork0.293 7916 -
all-8343 -
obs--93.3 %
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)
10.60680.37-0.26021.63380.15320.74370.01270.04320.012-0.0791-0.0161-0.058-0.0354-0.00730.00340.0460.0106-0.04970.17120.00340.076223.25611.37336.946
20.65530.0075-0.3430.6945-0.85581.72410.0584-0.0272-0.03040.0745-0.0211-0.0492-0.18610.1454-0.03720.0779-0.0361-0.04790.1547-0.02380.08616.826-3.99552.409
32.0336-1.7869-0.48773.28610.36580.7504-0.09380.0102-0.05350.6236-0.00970.5103-0.1237-0.03640.10350.2234-0.0130.09460.1513-0.02080.20133.90815.7456.448
40.54210.4304-0.09251.2618-0.17611.10950.0307-0.02360.0005-0.00310.0170.0723-0.1767-0.0893-0.04770.05480.0284-0.03820.1593-0.01780.08215.964-6.22651.712
50.94950.41740.04871.49010.33762.05380.0378-0.0235-0.06510.0797-0.06020.22430.1093-0.32340.02240.0355-0.0007-0.04890.17250.00430.1919-1.102-21.20751.974
628.748814.0652-26.40856.8838-12.921724.265-0.4778-1.5283-0.5302-0.4321-0.3694-0.2480.84811.40880.84721.2430.03480.09740.58480.05380.381826.33316.989-15.011
71.24120.2165-0.70781.70190.13611.1940.01510.02920.072-0.005-0.0085-0.0318-0.08170.0291-0.00660.0676-0.0222-0.06310.15440.00310.07035.2118.71-0.156
80.74730.7685-0.03722.1190.18820.6134-0.08970.0446-0.0319-0.23290.0351-0.08730.01930.01230.05460.0549-0.0098-0.02510.1886-0.00210.06792.5725.573-6.042
90.62270.1109-0.05561.7199-0.39930.85230.0499-0.08160.06030.28720.00080.1669-0.09050.0476-0.05080.087-0.0216-0.01850.1682-0.01340.0914-8.9432.83714.969
100.54340.4023-0.0921.47330.04610.84120.0297-0.0493-0.00170.0627-0.01270.1609-0.0126-0.0434-0.0170.03160.0187-0.03660.15220.00130.0927-15.823-11.9429.693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 223
2X-RAY DIFFRACTION2A224 - 329
3X-RAY DIFFRACTION3A330 - 386
4X-RAY DIFFRACTION4A387 - 540
5X-RAY DIFFRACTION5A541 - 622
6X-RAY DIFFRACTION6B-1 - 9
7X-RAY DIFFRACTION7B10 - 91
8X-RAY DIFFRACTION8B92 - 252
9X-RAY DIFFRACTION9B253 - 386
10X-RAY DIFFRACTION10B387 - 622

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