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- PDB-5fh0: The structure of rat cytosolic PEPCK variant E89A complex with GTP -

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Basic information

Entry
Database: PDB / ID: 5fh0
TitleThe structure of rat cytosolic PEPCK variant E89A complex with GTP
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / kinase / gluconeogenesis
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'-TRIPHOSPHATE / : / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsJohnson, T.A. / Holyoak, T.
Funding support United States, Canada, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Research Resources (NIH/NCRR)P20 RR17708 United States
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Biochemistry / Year: 2016
Title: Utilization of Substrate Intrinsic Binding Energy for Conformational Change and Catalytic Function in Phosphoenolpyruvate Carboxykinase.
Authors: Johnson, T.A. / Mcleod, M.J. / Holyoak, T.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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.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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3917
Polymers69,4421
Non-polymers9496
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-20 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.428, 85.710, 118.415
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 69441.625 Da / Num. of mol.: 1 / Mutation: E89A
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 , 5 types, 399 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-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 44.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 25% PEG 3350, 0.1M HEPES PH 7.4, 8MM MNCL2, 10mM GTP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→100 Å / Num. obs: 81130 / % possible obs: 99.2 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.018 / Rrim(I) all: 0.068 / Χ2: 1.061 / Net I/av σ(I): 37.105 / Net I/σ(I): 16.8 / Num. measured all: 1129880
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.6610.80.34474990.970.1070.3611.02692.9
1.66-1.7213.50.27381280.9850.0750.2841.002100
1.72-1.813.80.20980460.9890.0560.2171.017100
1.8-1.9140.16581000.9930.0450.1711.038100
1.9-2.0214.10.13581290.9940.0360.1391.076100
2.02-2.1714.40.11881110.9950.0310.1221.09100
2.17-2.3914.60.10381710.9960.0280.1071.056100
2.39-2.7414.80.07782090.9980.020.081.048100
2.74-3.4514.80.06882660.9980.0180.071.102100
3.45-10014.10.04784710.9990.0130.0491.13198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DT2

3dt2


Resolution: 1.6→69.43 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2706 / WRfactor Rwork: 0.2351 / FOM work R set: 0.8201 / SU B: 2.171 / SU ML: 0.076 / SU R Cruickshank DPI: 0.102 / SU Rfree: 0.0999 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 4053 5 %RANDOM
Rwork0.2007 72948 --
obs0.2023 77001 98.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.59 Å2 / Biso mean: 30.211 Å2 / Biso min: 14.46 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.6→69.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 51 393 5304
Biso mean--25.77 35.31 -
Num. residues----619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195122
X-RAY DIFFRACTIONr_bond_other_d0.0020.024850
X-RAY DIFFRACTIONr_angle_refined_deg1.481.976959
X-RAY DIFFRACTIONr_angle_other_deg0.935311231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3995640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91524.304230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69115876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8551529
X-RAY DIFFRACTIONr_chiral_restr0.0830.2729
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021160
X-RAY DIFFRACTIONr_mcbond_it1.7972.8592498
X-RAY DIFFRACTIONr_mcbond_other1.7972.8582497
X-RAY DIFFRACTIONr_mcangle_it2.7324.2813125
LS refinement shellResolution: 1.597→1.638 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 263 -
Rwork0.275 4702 -
all-4965 -
obs--82.6 %

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