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- PDB-2gmv: PEPCK complex with a GTP-competitive inhibitor -

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Basic information

Entry
Database: PDB / ID: 2gmv
TitlePEPCK complex with a GTP-competitive inhibitor
ComponentsPhosphoenolpyruvate carboxykinase, cytosolic
KeywordsLYASE / GLUCONEOGENESIS / XANTHINE / INHIBITOR
Function / homology
Function and homology information


cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / Abacavir metabolism / 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 ...cellular response to potassium ion starvation / protein serine kinase activity (using GTP as donor) / Abacavir metabolism / 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 / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / cellular response to fructose stimulus / 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 / Gluconeogenesis / glyceraldehyde-3-phosphate biosynthetic process / cellular hyperosmotic salinity response / cellular response to glucagon stimulus / response to starvation / cellular response to interleukin-1 / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / positive regulation of lipid biosynthetic process / cellular response to retinoic acid / cellular response to cAMP / cellular response to dexamethasone stimulus / response to activity / gluconeogenesis / cellular response to glucose stimulus / response to insulin / Transcriptional regulation of white adipocyte differentiation / cellular response to insulin stimulus / glucose metabolic process / GDP binding / 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 / extracellular exosome / 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
: / PHOSPHOENOLPYRUVATE / Chem-UN8 / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDunten, P.
Citation
Journal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: C-8 Modifications of 3-alkyl-1,8-dibenzylxanthines as inhibitors of human cytosolic phosphoenolpyruvate carboxykinase.
Authors: Pietranico, S.L. / Foley, L.H. / Huby, N. / Yun, W. / Dunten, P. / Vermeulen, J. / Wang, P. / Toth, K. / Ramsey, G. / Gubler, M.L. / Wertheimer, S.J.
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 2003
Title: X-ray structures of two xanthine inhibitors bound to PEPCK and N-3 modifications of substituted 1,8-dibenzylxanthines.
Authors: Foley, L.H. / Wang, P. / Dunten, P. / Ramsey, G. / Gubler, M.L. / Wertheimer, S.J.
#2: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of human cytosolic phosphoenolpyruvate carboxykinase reveals a new GTP-binding site.
Authors: Dunten, P. / Belunis, C. / Crowther, R. / Hollfelder, K. / Kammlott, U. / Levin, W. / Hanspeter, M. / Ramsey, G.B. / Swain, A. / Weber, D. / Wertheimer, S.J.
History
DepositionApr 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.4Feb 14, 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_label_seq_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
B: Phosphoenolpyruvate carboxykinase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,0717
Polymers139,0592
Non-polymers1,0125
Water2,378132
1
A: Phosphoenolpyruvate carboxykinase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3184
Polymers69,5301
Non-polymers7893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoenolpyruvate carboxykinase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7533
Polymers69,5301
Non-polymers2232
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.011, 66.134, 137.360
Angle α, β, γ (deg.)90.00, 145.09, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe enzyme is active as a monomer

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Components

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


Mass: 69529.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCK1 / Production host: Escherichia coli (E. coli)
References: UniProt: P35558, 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-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Chemical ChemComp-UN8 / N-(4-{[3-BUTYL-1-(2-FLUOROBENZYL)-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H-PURIN-8-YL]METHYL}PHENYL)-1-METHYL-1H-IMIDAZOLE-4-SULFONAMIDE


Mass: 565.619 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28FN7O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.39 Å3/Da / Density % sol: 48.56 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.3 Å / Biso Wilson estimate: 28.77 Å2

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data scaling
MOLREPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→39.31 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.856 / SU B: 10.758 / SU ML: 0.252 / ESU R: 0.825 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.287 2231 4.99 %
Rwork0.217 --
obs-44751 75.7 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.775 Å20 Å24.512 Å2
2---5.207 Å2-0 Å2
3----4.603 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9430 0 62 132 9624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_dihedral_angle_d11.95
X-RAY DIFFRACTIONf_angle_deg0.665
LS refinement shellResolution: 2.3→2.35 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.3853 49 -
Rwork0.264 1097 -
obs--29.5 %

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