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- PDB-9eiv: Rat cytosolic PEPCK in complex with GDP and phosphoglycolic acid ... -

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Basic information

Entry
Database: PDB / ID: 9eiv
TitleRat cytosolic PEPCK in complex with GDP and phosphoglycolic acid (253K)
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 / 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 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 / manganese ion binding / peptidyl-serine phosphorylation / cellular response to hypoxia / 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
GUANOSINE-5'-DIPHOSPHATE / : / 2-PHOSPHOGLYCOLIC ACID / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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

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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)70,2646
Polymers69,5001
Non-polymers7645
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.711, 119.789, 60.074
Angle α, β, γ (deg.)90.00, 111.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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 / Plasmid: pESUMOstar (KAN) / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.89 %
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, 100 mM GDP, and 18-28% PEG 3350

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Data collection

DiffractionMean temperature: 253 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: 1.92→60.08 Å / Num. obs: 44474 / % possible obs: 98.2 % / Redundancy: 6.69 % / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.032 / Rrim(I) all: 0.082 / Net I/σ(I): 10
Reflection shellResolution: 1.92→1.96 Å / Redundancy: 6.92 % / Rmerge(I) obs: 1.457 / Mean I/σ(I) obs: 0.3 / Num. unique obs: 2244 / CC1/2: 0.627 / Rpim(I) all: 0.595 / Rrim(I) all: 1.576 / % possible all: 97.18

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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: 1.92→55.9 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.229 2176 5.07 %
Rwork0.1882 --
obs0.1904 42946 94.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.92→55.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4869 0 40 145 5054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.521
X-RAY DIFFRACTIONf_dihedral_angle_d11.5081914
X-RAY DIFFRACTIONf_chiral_restr0.042720
X-RAY DIFFRACTIONf_plane_restr0.003902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.950.4838920.44561806X-RAY DIFFRACTION66
1.95-20.38871350.38642421X-RAY DIFFRACTION90
2-2.050.34581220.35812560X-RAY DIFFRACTION95
2.05-2.10.35421430.33092538X-RAY DIFFRACTION96
2.1-2.170.38191360.30022611X-RAY DIFFRACTION96
2.17-2.240.30261380.26742625X-RAY DIFFRACTION96
2.24-2.320.28211550.22852544X-RAY DIFFRACTION96
2.32-2.410.26251190.20912613X-RAY DIFFRACTION97
2.41-2.520.26611560.21422580X-RAY DIFFRACTION97
2.52-2.650.24881180.20842633X-RAY DIFFRACTION97
2.65-2.820.2531270.19112624X-RAY DIFFRACTION97
2.82-3.030.24771480.18522628X-RAY DIFFRACTION97
3.03-3.340.22121280.17922642X-RAY DIFFRACTION97
3.34-3.820.20871440.16282614X-RAY DIFFRACTION98
3.82-4.820.17771550.14262649X-RAY DIFFRACTION98
4.82-55.90.19171600.1542682X-RAY DIFFRACTION98
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)
12.15451.0765-0.78083.3407-0.06844.3894-0.13380.2311-0.288-0.3686-0.0865-0.0490.41320.08810.24530.3420.06470.02360.2721-0.01720.3512-0.8909-18.645-7.2082
22.56461.57610.32545.29050.64471.84140.16190.04110.0672-0.2727-0.1351-0.2441-0.10860.1694-0.01450.32420.02340.05640.38130.00720.25894.7578-5.9875-5.3152
30.4962-0.4931-0.02381.2070.5130.33290.00130.0292-0.05180.2456-0.07050.19130.0936-0.10380.06510.461-0.08360.0960.3795-0.04080.3953-9.5263-0.51439.1723
42.8178-1.0381-1.42055.1271-1.23932.47740.0564-0.2754-0.38010.9868-0.2478-0.29790.04240.86250.23750.7815-0.2276-0.04010.48830.02970.3541-0.9772-18.135821.4234
53.91330.6979-0.04962.3590.71493.0103-0.08380.0245-0.55440.27590.0144-0.20230.09170.14570.05660.29740.01310.04240.2030.03090.3057-5.44579.27814.4734
63.56620.1649-0.88852.0567-0.18392.0409-0.0513-0.31750.04930.3724-0.06-0.0803-0.13850.08810.10320.4729-0.0322-0.01830.24530.02510.3168-3.05617.279218.9492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 225 )
3X-RAY DIFFRACTION3chain 'A' and (resid 226 through 368 )
4X-RAY DIFFRACTION4chain 'A' and (resid 369 through 412 )
5X-RAY DIFFRACTION5chain 'A' and (resid 413 through 474 )
6X-RAY DIFFRACTION6chain 'A' and (resid 475 through 622 )

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