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- PDB-1m51: PEPCK complex with a GTP-competitive inhibitor -

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Basic information

Entry
Database: PDB / ID: 1m51
TitlePEPCK complex with a GTP-competitive inhibitor
Componentsphosphoenolpyruvate carboxykinase, cytosolic
KeywordsLYASE / gluconeogenesis / xanthine / inhibitor
Function / homology
Function and homology information


positive regulation of transcription from RNA polymerase II promoter in response to acidic pH / protein serine kinase activity (using GTP as donor) / cellular response to potassium ion starvation / Abacavir metabolism / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / propionate catabolic process / cellular response to fructose stimulus / phosphoenolpyruvate carboxykinase (GTP) ...positive regulation of transcription from RNA polymerase II promoter in response to acidic pH / protein serine kinase activity (using GTP as donor) / cellular response to potassium ion starvation / Abacavir metabolism / response to methionine / glycerol biosynthetic process from pyruvate / Transferases; Transferring phosphorus-containing groups; Protein-serine/threonine kinases / propionate catabolic process / cellular response to fructose stimulus / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / regulation of lipid biosynthetic process / response to interleukin-6 / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / carboxylic acid binding / oxaloacetate metabolic process / hepatocyte differentiation / positive regulation of memory T cell differentiation / Gluconeogenesis / cellular response to glucagon stimulus / response to starvation / response to lipid / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / cellular response to interleukin-1 / cellular response to dexamethasone stimulus / cellular response to retinoic acid / gluconeogenesis / response to activity / cellular response to cAMP / response to insulin / cellular response to glucose stimulus / Transcriptional regulation of white adipocyte differentiation / GDP binding / cellular response to insulin stimulus / glucose metabolic process / glucose homeostasis / cellular response to tumor necrosis factor / cellular response to hypoxia / manganese ion binding / response to lipopolysaccharide / aging / peptidyl-serine phosphorylation / GTP binding / magnesium ion binding / endoplasmic reticulum / mitochondrion / extracellular exosome / 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) signature. / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate Carboxykinase, domain 1 ...Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase; domain 2 / 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
ACETATE ION / : / Chem-TSX / Phosphoenolpyruvate carboxykinase, cytosolic [GTP]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / rigid-body refinement / Resolution: 2.25 Å
AuthorsFoley, L.H. / Wang, P. / Dunten, P. / Wertheimer, S.J.
Citation
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.
#1: 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. / Michel, H. / Ramsey, G.B. / Swain, A. / Weber, D. / Wertheimer, S.J.
History
DepositionJul 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: phosphoenolpyruvate carboxykinase, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1636
Polymers69,5301
Non-polymers6345
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.407, 61.067, 62.007
Angle α, β, γ (deg.)88.91, 70.21, 72.62
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 69529.703 Da / Num. of mol.: 1
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)

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Non-polymers , 5 types, 188 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-TSX / N-[4-(1-ALLYL-3-BUTYL-2,6-DIOXO-2,3,6,7-TETRAHYDRO-1H-PURIN-8-YLMETHYL)-PHENYL]-ACETAMIDE / 1-ALLYL-3-BUTYL-8-(N-ACETYL-4-AMINOBENZYL)-XANTHINE


Mass: 395.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H25N5O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growMethod: vapor diffusion / Details: VAPOR DIFFUSION
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 29, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 26567 / % possible obs: 94.1 % / Redundancy: 1.9 % / Rsym value: 0.044 / Net I/σ(I): 29.6
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 1.7 % / Rsym value: 0.06 / % possible all: 88.2

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.1.24refinement
RefinementMethod to determine structure: rigid-body refinement / Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.896 / SU B: 5.998 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.396
RfactorNum. reflection% reflectionSelection details
Rfree0.23665 1331 5 %RANDOM
Rwork0.17794 ---
obs0.18087 25224 94.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.051 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20.37 Å2-0.03 Å2
2--0.43 Å2-0.53 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4720 0 42 183 4945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214880
X-RAY DIFFRACTIONr_angle_refined_deg1.2371.966602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.175600
X-RAY DIFFRACTIONr_chiral_restr0.0810.2696
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023717
X-RAY DIFFRACTIONr_nbd_refined0.1960.22263
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.28
X-RAY DIFFRACTIONr_mcbond_it0.5851.53007
X-RAY DIFFRACTIONr_mcangle_it1.1324836
X-RAY DIFFRACTIONr_scbond_it1.82531873
X-RAY DIFFRACTIONr_scangle_it3.0074.51766
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.269 89
Rwork0.181 1694
obs-1783
Refinement
*PLUS
Rfactor Rwork: 0.181
Solvent computation
*PLUS
Displacement parameters
*PLUS

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