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- PDB-5v9h: Structure of the H477R variant of rat cytosolic PEPCK in complex ... -

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Basic information

Entry
Database: PDB / ID: 5v9h
TitleStructure of the H477R variant of rat cytosolic PEPCK in complex with phosphoglycolate and GDP.
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / phosphoenolpyruvate carboxykinase
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; 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'-DIPHOSPHATE / : / 2-PHOSPHOGLYCOLIC ACID / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsHolyoak, T. / Cui, D.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Biochemistry / Year: 2017
Title: Asymmetric Anchoring Is Required for Efficient Omega-Loop Opening and Closing in Cytosolic Phosphoenolpyruvate Carboxykinase.
Authors: Cui, D.S. / Broom, A. / Mcleod, M.J. / Meiering, E.M. / Holyoak, T.
History
DepositionMar 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.name
Revision 1.3Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_conn.ptnr2_symmetry

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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)140,85015
Polymers139,0372
Non-polymers1,81213
Water5,224290
1
A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5448
Polymers69,5191
Non-polymers1,0257
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3067
Polymers69,5191
Non-polymers7876
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.480, 119.433, 88.166
Angle α, β, γ (deg.)90.000, 105.300, 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


Mass: 69518.711 Da / Num. of mol.: 2 / Mutation: H477R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Production host: Escherichia coli (E. coli)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 6 types, 303 molecules

#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.21 Å3/Da / Density % sol: 44.32 % / Description: rods
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 24 - 34% PEG 3350 and 100mM HEPES, at pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→100 Å / Num. obs: 65917 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.054 / Rrim(I) all: 0.143 / Χ2: 1.074 / Net I/σ(I): 10.3 / Num. measured all: 458307
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.236.10.81965980.8460.3590.8951.094100
2.23-2.326.50.6960.9010.2950.7571.086100
2.32-2.426.80.5610.9410.2320.6081.067100
2.42-2.556.90.4850.9520.1990.5241.098100
2.55-2.717.10.3560.9760.1430.3841.07100
2.71-2.927.20.2660.9850.1060.2871.079100
2.92-3.217.30.1860.9890.0740.2011.053100
3.21-3.687.30.1290.9920.0510.1391.055100
3.68-4.637.20.090.9940.0370.0981.058100
4.63-1007.10.0690.9960.0290.0751.08599.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DTB

3dtb


Resolution: 2.15→85.04 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 10.772 / SU ML: 0.256 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.351 / ESU R Free: 0.249
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3318 5.1 %RANDOM
Rwork0.2412 ---
obs0.2435 62531 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 114.7 Å2 / Biso mean: 46.667 Å2 / Biso min: 24.52 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å2-0.71 Å2
2---2.87 Å20 Å2
3---3.87 Å2
Refinement stepCycle: final / Resolution: 2.15→85.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9584 0 92 290 9966
Biso mean--46.41 40.98 -
Num. residues----1220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199945
X-RAY DIFFRACTIONr_bond_other_d0.0010.029415
X-RAY DIFFRACTIONr_angle_refined_deg1.1791.97113481
X-RAY DIFFRACTIONr_angle_other_deg0.874321771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97551224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05124.123439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.264151691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4861560
X-RAY DIFFRACTIONr_chiral_restr0.0630.21415
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02111168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022232
LS refinement shellResolution: 2.137→2.192 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 194 -
Rwork0.403 3826 -
all-4020 -
obs--81.44 %

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