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- PDB-6yi9: Crystal structure of the rat cytosolic PCK1, acetylated on Lys244 -

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Basic information

Entry
Database: PDB / ID: 6yi9
TitleCrystal structure of the rat cytosolic PCK1, acetylated on Lys244
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE
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 / regulation of lipid biosynthetic process / tricarboxylic acid metabolic 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 / oxaloacetate metabolic process / hepatocyte differentiation / positive regulation of memory T cell differentiation / glyceraldehyde-3-phosphate biosynthetic process / 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 / gluconeogenesis / response to activity / 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, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal
Similarity search - Domain/homology
Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsLatorre-Muro, P. / Baeza, J. / Hurtado-Guerrero, R. / Hicks, T. / Delso, I. / Hernandez-Ruiz, C. / Velazquez-Campoy, A. / Lawton, A.J. / Angulo, J. / Denu, J.M. / Carrodeguas, J.A.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Self-acetylation at the active site of phosphoenolpyruvate carboxykinase (PCK1) controls enzyme activity.
Authors: Latorre-Muro, P. / Baeza, J. / Hurtado-Guerrero, R. / Hicks, T. / Delso, I. / Hernandez-Ruiz, C. / Velazquez-Campoy, A. / Lawton, A.J. / Angulo, J. / Denu, J.M. / Carrodeguas, J.A.
History
DepositionApr 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)70,78221
Polymers69,5411
Non-polymers1,24120
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The enzyme is monomeric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint65 kcal/mol
Surface area24720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.384, 85.225, 119.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 69540.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Note that Lys244 is acetylated. / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Production host: Escherichia coli (E. coli)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 44.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 magnesium formate HEPES pH 8 NaF

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 55039 / % possible obs: 87.3 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.091 / Net I/σ(I): 13.2
Reflection shellResolution: 1.75→1.84 Å / Num. unique obs: 9080 / CC1/2: 0.874

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QF2

2qf2


Resolution: 1.75→19.95 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.902 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.126 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21151 2167 3.9 %RANDOM
Rwork0.17037 ---
obs0.17201 52817 87.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.795 Å2
Baniso -1Baniso -2Baniso -3
1--1.01 Å20 Å20 Å2
2--1.87 Å20 Å2
3----0.85 Å2
Refinement stepCycle: 1 / Resolution: 1.75→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 0 80 435 5387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0155063
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174624
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.7766811
X-RAY DIFFRACTIONr_angle_other_deg0.5481.74810853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3325618
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.52920.65200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.54515746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8681529
X-RAY DIFFRACTIONr_chiral_restr0.0720.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215616
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02925
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8962.1592477
X-RAY DIFFRACTIONr_mcbond_other1.8962.1592478
X-RAY DIFFRACTIONr_mcangle_it2.8553.2323093
X-RAY DIFFRACTIONr_mcangle_other2.8553.2323094
X-RAY DIFFRACTIONr_scbond_it2.8022.5222586
X-RAY DIFFRACTIONr_scbond_other2.8022.5222586
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.333.6073719
X-RAY DIFFRACTIONr_long_range_B_refined8.73727.2625693
X-RAY DIFFRACTIONr_long_range_B_other8.73127.2615692
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 168 -
Rwork0.228 4446 -
obs--99.76 %

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