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- PDB-3dt7: The structure of rat cytosolic PEPCK in complex with beta-sulfopy... -

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Basic information

Entry
Database: PDB / ID: 3dt7
TitleThe structure of rat cytosolic PEPCK in complex with beta-sulfopyruvate and GTP
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / kinase / gluconeogenesis / Decarboxylase / GTP-binding / Nucleotide-binding
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 / tricarboxylic acid metabolic process / regulation of lipid biosynthetic 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 / glyceraldehyde-3-phosphate biosynthetic process / oxaloacetate metabolic process / hepatocyte differentiation / positive regulation of memory T cell differentiation / 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 / response to activity / gluconeogenesis / 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; 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
2-ETHOXYETHANOL / GUANOSINE-5'-TRIPHOSPHATE / : / SULFOPYRUVATE / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsSullivan, S.M. / Holyoak, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection.
Authors: Sullivan, S.M. / Holyoak, T.
History
DepositionJul 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _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_asym_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.ptnr3_auth_asym_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)141,40916
Polymers139,2882
Non-polymers2,12214
Water17,997999
1
A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8519
Polymers69,6441
Non-polymers1,2088
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5587
Polymers69,6441
Non-polymers9146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.019, 119.503, 87.283
Angle α, β, γ (deg.)90.000, 107.070, 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 / Phosphoenolpyruvate carboxylase


Mass: 69643.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Plasmid: PGEX4T2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P07379, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 7 types, 1013 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-SPV / SULFOPYRUVATE


Mass: 168.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O6S
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-ETX / 2-ETHOXYETHANOL


Mass: 90.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 999 / 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: 2.22 Å3/Da / Density % sol: 44.59 %
Crystal growTemperature: 298 K / Method: hanging drop vapor diffusion / pH: 7.4
Details: 12-30% PEG 3350, 0.1M HEPES, 10 MM MNCL2, pH 7.4, hanging drop vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2007 / Details: Bent conical Si-mirror (Rh coated)
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→100 Å / Num. obs: 187821 / % possible obs: 97.5 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.089 / Χ2: 1.018 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.5-1.554.60.695162911.073184.8
1.55-1.625.40.603182831.102195.2
1.62-1.6960.522189661.097198.8
1.69-1.786.50.401191461.139199.4
1.78-1.896.80.273191210.999199.5
1.89-2.046.90.181191050.954199.4
2.04-2.2470.117191670.924199.5
2.24-2.567.10.082192210.986199.7
2.56-3.237.20.061192750.941199.7
3.23-10070.036192461.043198.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 1.5→29.15 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.863 / SU B: 3.097 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 9440 5 %RANDOM
Rwork0.174 ---
obs0.176 187706 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.56 Å2 / Biso mean: 8.921 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.03 Å2
2--0.02 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9702 0 113 999 10814
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02210460
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.97414261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.28251349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62724.322479
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.542151824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.611565
X-RAY DIFFRACTIONr_chiral_restr0.1340.21493
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218078
X-RAY DIFFRACTIONr_mcbond_it1.0311.56335
X-RAY DIFFRACTIONr_mcangle_it1.713210274
X-RAY DIFFRACTIONr_scbond_it2.75934125
X-RAY DIFFRACTIONr_scangle_it4.384.53928
LS refinement shellResolution: 1.5→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 593 -
Rwork0.318 10961 -
all-11554 -
obs--81.35 %
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)
10.44310.1968-0.23640.7816-0.01240.46550.0362-0.0040.0389-0.0089-0.0114-0.0715-0.08220.0617-0.02480.0935-0.0033-0.01170.0567-0.00240.044338.51318.938-1.696
20.54920.49010.01041.08650.02820.4812-0.01780.0638-0.0066-0.06440.0212-0.04-0.02850.0368-0.00350.08840.0071-0.00070.08490.00040.055234.6865.858-6.129
30.39060.0361-0.08720.4083-0.37020.66280.0191-0.0149-0.01470.0421-0.0175-0.0046-0.05720.0724-0.00170.1044-0.0109-0.00370.0782-0.01450.060828.326-1.3099.312
41.5846-0.9416-0.15021.8542-0.25540.6722-0.0509-0.03120.01760.29370.02060.2316-0.1685-0.04130.03030.12140.01070.04330.0179-0.02830.080715.35219.47213.762
50.38690.15070.03340.5379-0.07050.66490.0166-0.0329-0.0340.02640.01090.0575-0.032-0.0919-0.02750.06710.0131-0.00590.0845-0.00030.076516.363-11.59810.21
60.65590.1384-0.350.8981-0.04810.51030.0212-0.00260.0458-0.0115-0.0237-0.0734-0.13710.10330.00250.1033-0.0274-0.01970.0684-0.00050.043419.33818.926-42.946
70.32010.3662-0.02931.1340.07640.4997-0.02050.05070.003-0.0932-0.0006-0.0257-0.06430.05350.02110.0642-0.0063-0.00510.09270.00390.045415.4465.906-48.504
80.48750.08670.0370.6871-0.25230.58320.0262-0.05650.04280.1018-0.02050.0434-0.06350.0533-0.00570.0931-0.01420.00460.0729-0.01490.05145.6253.125-30.015
90.36980.3179-0.01180.7664-0.01830.47040.0036-0.01630.05990.01160.00430.0989-0.0594-0.0122-0.00790.07970.01140.00170.078-0.00570.0611.053-4.229-34.656
100.44140.1594-0.02390.80750.16030.93930.0124-0.0379-0.02190.0805-0.04260.11670.0707-0.08490.03020.0605-0.0030.00450.06540.00670.0805-6.496-18-30.072
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 911 - 93
2X-RAY DIFFRACTION2AA92 - 20994 - 211
3X-RAY DIFFRACTION3AA210 - 348212 - 350
4X-RAY DIFFRACTION4AA349 - 387351 - 389
5X-RAY DIFFRACTION5AA388 - 622390 - 624
6X-RAY DIFFRACTION6BB4 - 916 - 93
7X-RAY DIFFRACTION7BB92 - 22394 - 225
8X-RAY DIFFRACTION8BB224 - 386226 - 388
9X-RAY DIFFRACTION9BB387 - 500389 - 502
10X-RAY DIFFRACTION10BB501 - 622503 - 624

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