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- PDB-5fh4: The structure of rat cytosolic PEPCK variant E89D in complex with... -

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Basic information

Entry
Database: PDB / ID: 5fh4
TitleThe structure of rat cytosolic PEPCK variant E89D in complex with beta-sulfopyruvate and 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 / : / SULFOPYRUVATE / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,4899
Polymers69,4861
Non-polymers1,0038
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-23 kcal/mol
Surface area24400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.590, 118.809, 60.508
Angle α, β, γ (deg.)90.000, 109.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 69485.633 Da / Num. of mol.: 1 / Mutation: e89d
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, 510 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-SPV / SULFOPYRUVATE


Mass: 168.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O6S
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
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: SSRL / Beamline: BL7-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.49→100 Å / Num. obs: 95906 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.088 / Χ2: 1.005 / Net I/av σ(I): 13.94 / Net I/σ(I): 13 / Num. measured all: 585490
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.555.90.51296251.0199.9
1.55-1.625.90.39595030.998100
1.62-1.6960.33195890.991100
1.69-1.7860.25995890.993100
1.78-1.896.10.19895820.997100
1.89-2.046.20.1695851.017100
2.04-2.246.20.13496271.029100
2.24-2.566.30.11195491.004100
2.56-3.236.30.08296310.985100
3.23-1006.30.05696261.02999.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DT7

3dt7


Resolution: 1.49→34.34 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.2286 / WRfactor Rwork: 0.2044 / FOM work R set: 0.7929 / SU B: 3.747 / SU ML: 0.074 / SU R Cruickshank DPI: 0.0873 / SU Rfree: 0.0851 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 4787 5 %RANDOM
Rwork0.2044 ---
obs0.2056 90947 99.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.65 Å2 / Biso mean: 23.33 Å2 / Biso min: 11.47 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.16 Å2
2---0.01 Å20 Å2
3---0.41 Å2
Refinement stepCycle: final / Resolution: 1.49→34.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4811 0 54 502 5367
Biso mean--20.22 29.17 -
Num. residues----612
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195089
X-RAY DIFFRACTIONr_bond_other_d0.0020.024826
X-RAY DIFFRACTIONr_angle_refined_deg1.6211.9726912
X-RAY DIFFRACTIONr_angle_other_deg0.968311171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17724.167228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.76315877
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6111531
X-RAY DIFFRACTIONr_chiral_restr0.0950.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215749
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021154
X-RAY DIFFRACTIONr_mcbond_it0.2090.5992481
X-RAY DIFFRACTIONr_mcbond_other0.2090.5992480
X-RAY DIFFRACTIONr_mcangle_it0.3740.8973106
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 348 -
Rwork0.326 6135 -
all-6483 -
obs--91.03 %
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)
12.04273.4711-1.71566.0662-4.07759.66920.13250.12220.12450.10210.09660.20150.77080.5468-0.22910.43580.03940.12010.31-0.04170.4424-17.0645-18.936159.1529
22.77810.1811-1.25013.745-1.43052.0746-0.0289-0.2358-0.13410.4712-0.0557-0.1323-0.00780.12910.08460.10630.0017-0.06940.18980.03010.1271-7.2874-17.10644.1187
34.1669-0.943-1.16161.91150.87332.1651-0.1216-0.1365-0.3476-0.28390.0454-0.11940.3647-0.03650.07610.2222-0.0095-0.00270.14060.00790.1532-9.2676-20.566921.2482
40.9264-0.5645-0.15962.5972-0.92491.1538-0.0432-0.072-0.03870.18170.01960.1347-0.0328-0.03450.02360.0397-0.0029-0.03310.18230.00740.0953-15.0772-5.879633.5416
51.17951.0456-0.58131.7787-1.0280.9779-0.0617-0.1221-0.0906-0.1488-0.0722-0.16220.07760.08970.13390.0430.0221-0.03680.1670.01290.1137-1.28742.40120.5684
60.9173-0.12310.5933.58631.4212.9694-0.05610.1319-0.1978-0.81370.0481-0.38820.11770.05620.0080.4411-0.01210.13520.1115-0.02390.1741-5.485-19.6248.1756
74.76580.028-0.13664.1097-0.10011.308-0.19430.5578-0.406-1.1244-0.01280.34930.3108-0.32640.20710.4688-0.0377-0.02710.2537-0.05320.1487-13.073-17.15377.6752
81.419-0.265-0.5221.2959-0.48081.2988-0.02620.0077-0.1163-0.0661-0.01240.0004-0.0544-0.02570.03860.04490.0063-0.04350.1333-0.00510.089-6.406111.224817.2821
92.7049-0.0288-0.00671.82380.56721.9398-0.08390.09120.1141-0.2204-0.0512-0.08380.00310.06050.13510.07620.0042-0.03570.14840.0280.0783-0.313514.36755.3616
101.4911-0.02-0.5681.8547-0.84042.00310.05760.25310.0218-0.4414-0.09320.0812-0.1841-0.16330.03560.22390.0365-0.08520.1845-0.00580.1166-12.489121.27216.5126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 9
2X-RAY DIFFRACTION2A10 - 53
3X-RAY DIFFRACTION3A54 - 91
4X-RAY DIFFRACTION4A92 - 223
5X-RAY DIFFRACTION5A224 - 349
6X-RAY DIFFRACTION6A350 - 387
7X-RAY DIFFRACTION7A388 - 409
8X-RAY DIFFRACTION8A410 - 502
9X-RAY DIFFRACTION9A503 - 559
10X-RAY DIFFRACTION10A560 - 622

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