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- PDB-9ej2: Rat cytosolic PEPCK in complex with GTP and oxalate (313K) -

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Basic information

Entry
Database: PDB / ID: 9ej2
TitleRat cytosolic PEPCK in complex with GTP and oxalate (313K)
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / Inhibitor complex / Metabolic enzyme / Multi-temperature / Ambient temperature
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, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / : / OXALATE ION / TRIETHYLENE GLYCOL / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsMcLeod, M.J. / Barwell, S.A.E. / Holyoak, T. / Thorne, R.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DBI-2210041 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM127528-02 United States
CitationJournal: Structure / Year: 2025
Title: A structural perspective on the temperature dependent activity of enzymes.
Authors: McLeod, M.J. / Barwell, S.A.E. / Holyoak, T. / Thorne, R.E.
History
DepositionNov 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)70,4267
Polymers69,5001
Non-polymers9266
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.296, 120.160, 61.118
Angle α, β, γ (deg.)90.00, 111.47, 90.00
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: 69499.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 5 types, 208 molecules

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


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-OXL / OXALATE ION


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.77 %
Crystal growTemperature: 313 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 0.5 uL of 100 mM MnCl2, 10 mM GTP, and 18-28% PEG 3350

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Data collection

DiffractionMean temperature: 313 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.11→119.82 Å / Num. obs: 34331 / % possible obs: 99.56 % / Redundancy: 6.57 % / CC1/2: 0.996 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.047 / Rrim(I) all: 0.121 / Net I/σ(I): 6.2
Reflection shellResolution: 2.11→2.15 Å / Redundancy: 6.33 % / Rmerge(I) obs: 1.436 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 1714 / CC1/2: 0.614 / Rpim(I) all: 0.615 / Rrim(I) all: 1.564 / % possible all: 98.85

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→56.88 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.32 / Phase error: 27.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 1686 4.98 %
Rwork0.1891 --
obs0.1912 33839 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→56.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4869 0 51 202 5122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.505
X-RAY DIFFRACTIONf_dihedral_angle_d11.6361911
X-RAY DIFFRACTIONf_chiral_restr0.042719
X-RAY DIFFRACTIONf_plane_restr0.004898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.180.35581370.32962473X-RAY DIFFRACTION91
2.18-2.250.32731300.30822615X-RAY DIFFRACTION96
2.25-2.330.35471270.29892686X-RAY DIFFRACTION98
2.33-2.420.34491500.28512657X-RAY DIFFRACTION98
2.42-2.530.33551360.2722714X-RAY DIFFRACTION99
2.53-2.670.29541420.24922709X-RAY DIFFRACTION99
2.67-2.840.23671430.22662669X-RAY DIFFRACTION99
2.84-3.050.26251450.20812730X-RAY DIFFRACTION99
3.05-3.360.25911490.19012675X-RAY DIFFRACTION99
3.36-3.850.19391290.15832758X-RAY DIFFRACTION99
3.85-4.850.1791400.1372711X-RAY DIFFRACTION99
4.85-56.880.19291580.15462756X-RAY DIFFRACTION99
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)
11.64590.6776-0.57133.69190.56952.7395-0.00420.11490.0082-0.41590.0717-0.2816-0.1040.4136-0.02650.37980.00040.01580.3669-0.0160.32424.2242-11.2506-6.966
20.7944-0.47590.15022.39360.39020.938-0.0189-0.0137-0.09280.16660.07160.08140.0130.0736-0.01650.4133-0.07580.04230.3253-0.01250.34915.7858-3.88610.9548
34.58320.7516-0.68563.70970.08522.5659-0.1146-0.2342-0.06350.16860.0341-0.2189-0.02530.13310.0630.4746-0.0171-0.01220.21680.03560.345520.197416.350818.7561
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 206 )
2X-RAY DIFFRACTION2chain 'A' and (resid 207 through 443 )
3X-RAY DIFFRACTION3chain 'A' and (resid 444 through 622 )

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