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- PDB-9ej1: Rat cytosolic PEPCK in complex with GTP and oxalate (293K) -

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Basic information

Entry
Database: PDB / ID: 9ej1
TitleRat cytosolic PEPCK in complex with GTP and oxalate (293K)
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / Inhibitor complex / Metabolic enzyme / Multi-temperature / Ambient temperature
Function / homology
Function and homology information


response to methionine / Gluconeogenesis / 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 ...response to methionine / Gluconeogenesis / 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 / cellular hypotonic salinity response / carboxylic acid binding / 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 / nucleoside diphosphate kinase activity / cellular hyperosmotic salinity response / response to starvation / response to lipid / cellular response to interleukin-1 / cellular response to dexamethasone stimulus / positive regulation of lipid biosynthetic process / cellular response to retinoic acid / cellular response to glucagon stimulus / cellular response to cAMP / response to activity / gluconeogenesis / response to bacterium / cellular response to glucose stimulus / response to nutrient levels / response to insulin / peptidyl-serine phosphorylation / lipid metabolic process / glucose metabolic process / cellular response to insulin stimulus / cellular response to tumor necrosis factor / GDP binding / glucose homeostasis / manganese ion binding / response to lipopolysaccharide / cellular response to hypoxia / GTP binding / magnesium ion binding / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / cytoplasm / cytosol
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 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
Water3,063170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.315, 119.834, 60.826
Angle α, β, γ (deg.)90.00, 111.66, 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, 176 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.: 170 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 293 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: 293 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→120 Å / Num. obs: 40613 / % possible obs: 100 % / Redundancy: 6.82 % / CC1/2: 0.972 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.105 / Rrim(I) all: 0.276 / Net I/σ(I): 2.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.765 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2065 / CC1/2: 0.61 / Rpim(I) all: 0.723 / Rrim(I) all: 1.91 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→56.53 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 2032 5.01 %
Rwork0.1794 --
obs0.1811 40573 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→56.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4869 0 51 170 5090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.567
X-RAY DIFFRACTIONf_dihedral_angle_d12.9051912
X-RAY DIFFRACTIONf_chiral_restr0.044720
X-RAY DIFFRACTIONf_plane_restr0.004901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.32671590.29062501X-RAY DIFFRACTION98
2.05-2.10.33441300.27562582X-RAY DIFFRACTION100
2.1-2.160.31331430.26762577X-RAY DIFFRACTION100
2.16-2.220.31991270.24712522X-RAY DIFFRACTION100
2.22-2.290.26761170.23452585X-RAY DIFFRACTION100
2.29-2.370.23941170.21032611X-RAY DIFFRACTION100
2.37-2.470.21551210.20892546X-RAY DIFFRACTION100
2.47-2.580.26681530.20312561X-RAY DIFFRACTION100
2.58-2.720.25841290.19512567X-RAY DIFFRACTION100
2.72-2.890.23331270.18332584X-RAY DIFFRACTION100
2.89-3.110.22951400.17532567X-RAY DIFFRACTION100
3.11-3.420.19621620.1582569X-RAY DIFFRACTION100
3.42-3.920.15641240.14672563X-RAY DIFFRACTION100
3.92-4.930.14761450.14282590X-RAY DIFFRACTION100
4.94-56.530.21341380.17292616X-RAY DIFFRACTION100
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)
11.62731.1452-0.7074.6940.57992.20270.03080.0201-0.0284-0.2476-0.0038-0.2551-0.0260.3113-0.00270.19640.0252-0.02650.3398-0.02070.254924.8-10.9028-5.6369
21.12710.1066-0.0122.94940.49611.15650.0402-0.0912-0.09530.5618-0.08190.25080.11360.08670.04520.2682-0.06710.04680.2652-0.0330.246114.8123-4.833811.9389
33.43230.4601-0.65883.58730.63021.7921-0.0487-0.2197-0.07030.5425-0.0342-0.015-0.00620.15510.05380.3656-0.0271-0.01440.17220.03880.212218.622414.937617.7147
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 225 )
2X-RAY DIFFRACTION2chain 'A' and (resid 226 through 412 )
3X-RAY DIFFRACTION3chain 'A' and (resid 413 through 622 )

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