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- PDB-2rkd: The Structure of rat cytosolic PEPCK in complex with 3-phosphonop... -

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Basic information

Entry
Database: PDB / ID: 2rkd
TitleThe Structure of rat cytosolic PEPCK in complex with 3-phosphonopropionate
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic [GTP]
KeywordsLYASE / kinase / gluconeogenesis / Decarboxylase / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / 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 / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process ...Gluconeogenesis / phosphoenolpyruvate carboxykinase activity / cellular response to potassium ion starvation / 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 / 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 hypotonic response / cellular response to fructose stimulus / cellular hypotonic salinity response / glyceraldehyde-3-phosphate biosynthetic process / carboxylic acid binding / cellular response to phorbol 13-acetate 12-myristate / oxaloacetate metabolic process / hepatocyte differentiation / cellular hyperosmotic response / positive regulation of memory T cell differentiation / nucleoside diphosphate kinase activity / cellular hyperosmotic salinity response / response to lipid / response to starvation / cellular response to glucagon stimulus / positive regulation of lipid biosynthetic process / cellular response to interleukin-1 / cellular response to retinoic acid / cellular response to cAMP / 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 / GDP binding / glucose metabolic process / glucose homeostasis / cellular response to tumor necrosis factor / 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
3-PHOSPHONOPROPANOIC ACID / : / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsSullivan, S.M. / Stiffin, R.M. / Carlson, G.M. / Holyoak, T.
CitationJournal: Biochemistry / Year: 2008
Title: Differential Inhibition of Cytosolic PEPCK by Substrate Analogues. Kinetic and Structural Characterization of Inhibitor Recognition.
Authors: Stiffin, R.M. / Sullivan, S.M. / Carlson, G.M. / Holyoak, T.
History
DepositionOct 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 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 / 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 / _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]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9315
Polymers69,6441
Non-polymers2874
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.294, 119.397, 60.762
Angle α, β, γ (deg.)90.000, 108.660, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 69643.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pck1 / Plasmid: PGEX4T2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (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.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-3PP / 3-PHOSPHONOPROPANOIC ACID / 2-CARBOXYETHYLPHOSPHONIC ACID


Mass: 154.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O5P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.24 Å3/Da / Density % sol: 44.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 12-30% PEG 3350, 0.1M HEPES, 10 MM MNCL2, pH 7.4, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 23, 2007 / Details: BLUE OSMIC Confocal MIRRORS
RadiationMonochromator: Blue osmic mirrors / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 46838 / % possible obs: 97.2 % / Redundancy: 7 % / Rmerge(I) obs: 0.092 / Χ2: 1.081 / Net I/σ(I): 14.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.975.50.65340651.097184.2
1.97-2.056.20.50645101.083194.9
2.05-2.146.80.39446801.074197.7
2.14-2.257.20.30447561.078198.3
2.25-2.397.30.22747371.064198.8
2.39-2.587.30.17547461.082199.2
2.58-2.847.30.13248371.071199.4
2.84-3.257.40.147901.033199.8
3.25-4.097.40.07348381.0881100
4.09-1007.40.04948791.148199.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
CrystalCleardata collection
RefinementResolution: 1.9→33.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 7.86 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2377 5.1 %RANDOM
Rwork0.187 ---
obs0.189 46794 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.395 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.01 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4819 0 12 471 5302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225052
X-RAY DIFFRACTIONr_angle_refined_deg1.1121.9646856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7495637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19524.174230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.04315880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1921532
X-RAY DIFFRACTIONr_chiral_restr0.0780.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023888
X-RAY DIFFRACTIONr_nbd_refined0.180.22408
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23399
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2441
X-RAY DIFFRACTIONr_metal_ion_refined0.1360.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.238
X-RAY DIFFRACTIONr_mcbond_it0.3621.53094
X-RAY DIFFRACTIONr_mcangle_it0.66924995
X-RAY DIFFRACTIONr_scbond_it1.03832052
X-RAY DIFFRACTIONr_scangle_it1.7114.51849
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 157 -
Rwork0.304 2711 -
all-2868 -
obs--81.43 %
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)
15.3362-3.6679-7.906520.0149-5.520518.57530.9344-0.00032.3944-1.6689-0.8606-2.15841.0077-0.9333-0.07380.1909-0.21670.24860.2963-0.09810.19365.5892-18.782-28.7281
21.95250.4525-0.51693.03210.68251.5853-0.05510.18580.0218-0.26410.05180.24550.075-0.03690.00330.0098-0.0081-0.05250.0736-0.02350.0219-2.9543-17.1016-15.0776
33.16770.69390.05753.17250.27561.670.06990.0733-0.30940.5394-0.0840.22970.3609-0.00740.01410.1931-0.02790.0188-0.04640.0071-0.0196-1.623-22.90248.0094
41.73020.79510.50173.43652.04323.4594-0.0958-0.01370.01770.10620.0992-0.3573-0.13490.1378-0.0034-0.0396-0.0054-0.05710.10970.00390.078214.11488.39061.0048
51.95850.06260.308714.91764.33671.30380.11970.14740.1875-0.2619-0.0637-0.6776-0.0585-0.0085-0.056-0.0618-0.0062-0.00240.10980.00060.079315.9792-3.5234-9.1229
61.1140.16890.11392.08910.35360.78470.01880.11790.01320.0926-0.07530.11120.07190.02750.05640.0045-0.0077-0.01810.0949-0.01650.04440.3505-11.1235-5.4404
70.7821-0.6665-0.210.64630.40580.7144-0.0170.1394-0.07740.1871-0.10170.1826-0.005-0.02750.11860.0261-0.02940.02110.075-0.02620.1065-5.4393.25034.1122
81.73581.7388-0.72772.4157-2.52545.0934-0.3408-0.2831-0.84920.0375-0.0998-0.34720.2940.15340.44060.169-0.0360.162-0.07670.01350.1001-12.29341.037521.3863
90.6788-0.5902-0.2251.78640.54360.575-0.13340.1241-0.02760.1706-0.14310.19650.1852-0.1870.27650.0254-0.05370.06970.0632-0.04520.1137-12.93073.35417.7008
101.124-0.63460.88513.0172-0.10721.65840.026-0.1436-0.081.1688-0.01310.4740.1304-0.1364-0.01290.428-0.07290.2084-0.07410.0172-0.0332-6.7692-17.261721.4759
114.2607-1.2333-0.04832.99040.20270.91190.0613-0.5336-0.16110.8819-0.02380.02560.26090.1585-0.03750.3387-0.06590.07470.02350.017-0.0387-0.6732-15.799618.5907
121.26520.0304-0.2940.8170.57821.1698-0.0641-0.0085-0.1230.19810.00090.06190.08790.06990.06320.0668-0.0161-0.01270.04230.01950.0419-1.534412.187512.3305
132.64430.28280.07031.4166-0.05661.2982-0.0802-0.1867-0.02410.2323-0.0910.11910.0695-0.01660.17120.0842-0.00240.01620.0507-0.0170.0126-9.980815.103822.4953
140.0065-0.0433-0.12850.28720.85182.52660.4259-2.4166-0.1826-0.2118-0.09740.449-0.64880.0007-0.32850.2334-0.06490.08060.35470.11630.2427-11.477513.550535.466
150.8009-0.687-0.92741.92181.082.1881-0.0287-0.07980.10880.24290.0752-0.1844-0.12290.1325-0.04650.0545-0.0289-0.07950.04970.00820.05117.716324.312717.1043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 115 - 13
2X-RAY DIFFRACTION2AA12 - 5414 - 56
3X-RAY DIFFRACTION3AA55 - 8757 - 89
4X-RAY DIFFRACTION4AA88 - 11490 - 116
5X-RAY DIFFRACTION5AA115 - 133117 - 135
6X-RAY DIFFRACTION6AA134 - 225136 - 227
7X-RAY DIFFRACTION7AA226 - 285228 - 287
8X-RAY DIFFRACTION8AA286 - 302288 - 304
9X-RAY DIFFRACTION9AA303 - 338305 - 340
10X-RAY DIFFRACTION10AA339 - 383341 - 385
11X-RAY DIFFRACTION11AA384 - 418386 - 420
12X-RAY DIFFRACTION12AA419 - 499421 - 501
13X-RAY DIFFRACTION13AA500 - 560502 - 562
14X-RAY DIFFRACTION14AA561 - 578563 - 580
15X-RAY DIFFRACTION15AA579 - 622581 - 624

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