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- PDB-2rka: The Structure of rat cytosolic PEPCK in complex with phosphoglycolate -

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Basic information

Entry
Database: PDB / ID: 2rka
TitleThe Structure of rat cytosolic PEPCK in complex with phosphoglycolate
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 / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / glycerol biosynthetic process from pyruvate / 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 / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / glycerol biosynthetic process from pyruvate / 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 / oxaloacetate metabolic process / hepatocyte differentiation / positive regulation of memory T cell differentiation / glyceraldehyde-3-phosphate biosynthetic process / cellular hyperosmotic response / nucleoside diphosphate kinase activity / cellular hyperosmotic salinity response / response to lipid / response to starvation / cellular response to glucagon stimulus / cellular response to interleukin-1 / positive regulation of lipid biosynthetic process / cellular response to retinoic acid / cellular response to cAMP / response to nutrient levels / cellular response to dexamethasone stimulus / 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
: / 2-PHOSPHOGLYCOLIC ACID / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 1.95 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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_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]
C: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,86510
Polymers139,2882
Non-polymers5788
Water18,3391018
1
A: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9335
Polymers69,6441
Non-polymers2894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,9335
Polymers69,6441
Non-polymers2894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.670, 119.660, 90.867
Angle α, β, γ (deg.)90.00, 108.90, 90.00
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.: 2
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-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5O6P
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1018 / 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: 45.1 %
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: May 29, 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: 1.95→100 Å / Num. obs: 86353 / % possible obs: 96.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.105 / Χ2: 1.054 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.026.30.70584101.069194.6
2.02-2.16.50.54884081.109194.1
2.1-2.26.60.39883241.087193.8
2.2-2.316.60.32482671.053192.6
2.31-2.466.50.24484291.056194.2
2.46-2.656.60.19486761.066197
2.65-2.916.80.13888791.006199.3
2.91-3.337.30.09589341.076199.9
3.33-4.27.60.06789791.031100
4.2-1007.60.04690471.005199.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementResolution: 1.95→29.92 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 7.678 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 4327 5 %RANDOM
Rwork0.183 ---
obs0.185 86305 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.115 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.15 Å2
2---0.12 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9636 0 24 1018 10678
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210368
X-RAY DIFFRACTIONr_angle_refined_deg1.1251.96814112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.62551342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06424.183471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.682151858
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7041567
X-RAY DIFFRACTIONr_chiral_restr0.0780.21477
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027999
X-RAY DIFFRACTIONr_nbd_refined0.1870.25139
X-RAY DIFFRACTIONr_nbtor_refined0.3020.26939
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2973
X-RAY DIFFRACTIONr_metal_ion_refined0.1050.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.2130
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.248
X-RAY DIFFRACTIONr_mcbond_it0.3831.56311
X-RAY DIFFRACTIONr_mcangle_it0.706210238
X-RAY DIFFRACTIONr_scbond_it1.15634245
X-RAY DIFFRACTIONr_scangle_it1.8814.53819
LS refinement shellResolution: 1.95→1.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 307 -
Rwork0.254 5799 -
all-6106 -
obs--92.97 %
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)
12.14131.2513-0.77293.92021.57272.15870.0646-0.2739-0.01320.0610.1729-0.57460.00220.3362-0.2375-0.0534-0.035-0.00610.0226-0.0466-0.082441.66416.66628.36
21.7582-1.0781-0.56111.73990.55482.60430.1056-0.02640.2806-0.13670.00280.234-0.49210.0255-0.10840.0351-0.03150.0268-0.0613-0.0222-0.036916.93120.63122.56
30.78450.3077-0.16761.89690.6181.46060.02130.00440.0606-0.0841-0.0107-0.06290.00140.0851-0.0106-0.0721-0.01060.0109-0.06170.0009-0.199829.5425.85618.748
42.1530.2733-1.07930.3508-0.0831.77380.1212-0.08070.1337-0.0122-0.00340.0474-0.0640.016-0.1178-0.0377-0.01390.0027-0.0891-0.019-0.211411.158-6.13130.038
52.2345-1.33470.96913.5816-1.13861.54750.0447-0.00820.09280.03980.02130.8321-0.1891-0.2176-0.0661-0.00360.02880.0102-0.0443-0.030.09082.00315.89322.171
60.35670.7965-0.61973.7994-1.23621.96230.09660.0290.2521-0.17340.10140.5796-0.1374-0.1957-0.198-0.09330.0325-0.016-0.0147-0.0258-0.03667.2699.7122.932
71.65330.4263-0.37540.61240.36641.54820.020.06130.0069-0.16670.02580.0384-0.0981-0.0742-0.0458-0.03610.0196-0.0173-0.11650.0019-0.223511.259-13.8416.61
82.0097-0.5914-0.8871.87410.29993.42410.14610.09570.0685-0.1442-0.1490.1176-0.0451-0.33960.0029-0.0517-0.0066-0.0447-0.0632-0.0091-0.2117-0.892-12.76923.81
90.86390.1341-1.23163.36560.94644.73470.13210.0515-0.0508-0.0236-0.27280.47870.2573-0.84670.1407-0.0388-0.0422-0.0960.138-0.0403-0.0829-8.611-19.06419.594
102.97051.45170.65462.87250.45471.2166-0.1090.2169-0.1756-0.40860.0868-0.05670.0793-0.02440.02230.06040.019-0.0198-0.0843-0.0234-0.20411.827-24.5899.092
112.96461.5401-0.7042.61530.33021.39410.0204-0.1339-0.11080.23040.0848-0.57230.01050.2613-0.1052-0.0081-0.0036-0.0589-0.0192-0.0232-0.106926.30416.84370.533
122.9393-0.03930.38011.3293-0.05151.4193-0.0722-0.10730.415-0.0536-0.0420.3127-0.3684-0.10640.11420.03790.0209-0.0391-0.0643-0.0168-0.08161.57421.88465.091
131.48021.35141.32094.69942.48283.75410.00220.0979-0.2264-0.42690.1989-0.39780.14360.1355-0.201-0.0261-0.02220.0392-0.0177-0.0234-0.191313.331-10.1750.875
141.51360.7785-0.45272.26790.36331.3906-0.0354-0.01-0.0274-0.03460.0072-0.16270.02180.08420.0282-0.0818-0.0032-0.0122-0.081-0.011-0.221415.099.8963.848
151.26421.0097-0.39841.6351-0.3420.92560.064-0.06020.0610.0758-0.04690.07250.04310.022-0.0171-0.03110.00020.0049-0.0664-0.0361-0.22413.757-2.0165.606
160.36290.6693-0.20351.9352-0.08770.82180.0112-0.08260.22290.0363-0.07290.4395-0.0197-0.22550.0617-0.02050.01370.00930.007-0.062-0.1022-10.2137.04368.503
172.277-0.5276-1.00234.77840.35545.22410.090.58040.1602-0.7489-0.13570.7386-0.3877-0.66340.04570.01420.0634-0.14630.1131-0.02950.0057-9.41517.35155.213
181.10520.3152-0.10331.21770.5991.10540.0426-0.01440.01610.0225-0.00990.1175-0.078-0.0391-0.0327-0.04770.0206-0.0013-0.10880.0125-0.2195-4.169-11.01262.189
192.4272-0.0866-0.01651.85110.80563.00320.0466-0.0253-0.0150.0643-0.17210.36490.086-0.28830.1255-0.0203-0.02810.0247-0.0522-0.0202-0.1354-16.712-15.28565.506
201.81520.07090.11632.10350.20621.33490.01440.0484-0.1733-0.1032-0.05930.41650.0749-0.20030.0449-0.00060.0074-0.046-0.0734-0.0078-0.1387-10.697-21.74453.467
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 476 - 49
2X-RAY DIFFRACTION2AA48 - 9150 - 93
3X-RAY DIFFRACTION3AA92 - 24194 - 243
4X-RAY DIFFRACTION4AA242 - 329244 - 331
5X-RAY DIFFRACTION5AA330 - 385332 - 387
6X-RAY DIFFRACTION6AA386 - 430388 - 432
7X-RAY DIFFRACTION7AA431 - 500433 - 502
8X-RAY DIFFRACTION8AA501 - 546503 - 548
9X-RAY DIFFRACTION9AA547 - 585549 - 587
10X-RAY DIFFRACTION10AA586 - 622588 - 624
11X-RAY DIFFRACTION11CB4 - 486 - 50
12X-RAY DIFFRACTION12CB49 - 8951 - 91
13X-RAY DIFFRACTION13CB90 - 11392 - 115
14X-RAY DIFFRACTION14CB114 - 212116 - 214
15X-RAY DIFFRACTION15CB213 - 295215 - 297
16X-RAY DIFFRACTION16CB296 - 383298 - 385
17X-RAY DIFFRACTION17CB384 - 412386 - 414
18X-RAY DIFFRACTION18CB413 - 499415 - 501
19X-RAY DIFFRACTION19CB500 - 562502 - 564
20X-RAY DIFFRACTION20CB563 - 622565 - 624

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