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- PDB-8pq0: Structure of human PARK7 in complex with GK16R -

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Basic information

Entry
Database: PDB / ID: 8pq0
TitleStructure of human PARK7 in complex with GK16R
ComponentsParkinson disease protein 7
KeywordsHYDROLASE / Parkinson disease protein 7 / cyanopyrrolidine / DJ-1
Function / homology
Function and homology information


tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / guanine deglycation, glyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly ...tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal removal / guanine deglycation, glyoxal removal / cellular detoxification of methylglyoxal / regulation of supramolecular fiber organization / negative regulation of death-inducing signaling complex assembly / negative regulation of TRAIL-activated apoptotic signaling pathway / positive regulation of L-dopa biosynthetic process / glyoxalase (glycolic acid-forming) activity / negative regulation of protein K48-linked deubiquitination / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / glycolate biosynthetic process / detection of oxidative stress / glyoxal metabolic process / guanine deglycation / negative regulation of protein acetylation / methylglyoxal metabolic process / detoxification of mercury ion / ubiquitin-protein transferase inhibitor activity / protein deglycase / mercury ion binding / protein deglycase activity / positive regulation of dopamine biosynthetic process / oxidoreductase activity, acting on peroxide as acceptor / positive regulation of autophagy of mitochondrion / superoxide dismutase copper chaperone activity / positive regulation of mitochondrial electron transport, NADH to ubiquinone / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / lactate biosynthetic process / positive regulation of acute inflammatory response to antigenic stimulus / protein repair / peptidase inhibitor activity / cellular detoxification of aldehyde / peroxiredoxin activity / small protein activating enzyme binding / Hydrolases; Acting on ester bonds; Thioester hydrolases / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / detoxification of copper ion / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of protein sumoylation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of protein export from nucleus / membrane hyperpolarization / cupric ion binding / regulation of androgen receptor signaling pathway / insulin secretion / oxygen sensor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / nuclear androgen receptor binding / hydrogen peroxide metabolic process / positive regulation of reactive oxygen species biosynthetic process / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / cytokine binding / signaling receptor activator activity / cuprous ion binding / regulation of synaptic vesicle endocytosis / androgen receptor signaling pathway / negative regulation of protein phosphorylation / membrane depolarization / single fertilization / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of peptidyl-serine phosphorylation / regulation of neuron apoptotic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / removal of superoxide radicals / SUMOylation of transcription cofactors / enzyme activator activity / regulation of mitochondrial membrane potential / adult locomotory behavior / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / adherens junction / mitochondrion organization / positive regulation of protein-containing complex assembly / Late endosomal microautophagy / PML body / mitochondrial intermembrane space / positive regulation of protein localization to nucleus / autophagy / cellular response to hydrogen peroxide / kinase binding / Chaperone Mediated Autophagy / Aggrephagy / positive regulation of reactive oxygen species metabolic process / synaptic vesicle / glucose homeostasis / peptidase activity / cell body / cellular response to oxidative stress / regulation of inflammatory response
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / : / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
Chem-8RX / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsGrethe, C. / Gersch, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GE 3110/1-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: N-Cyanopiperazines as Specific Covalent Inhibitors of the Deubiquitinating Enzyme UCHL1.
Authors: Schmidt, M. / Grethe, C. / Recknagel, S. / Kipka, G.M. / Klink, N. / Gersch, M.
History
DepositionJul 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Parkinson disease protein 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3112
Polymers20,0711
Non-polymers2391
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8420 Å2
Unit cell
Length a, b, c (Å)66.722, 66.722, 176.528
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

21A-483-

HOH

31A-515-

HOH

41A-527-

HOH

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Components

#1: Protein Parkinson disease protein 7 / Maillard deglycase / Oncogene DJ1 / Parkinsonism-associated deglycase / Protein DJ-1 / DJ-1 / ...Maillard deglycase / Oncogene DJ1 / Parkinsonism-associated deglycase / Protein DJ-1 / DJ-1 / Protein/nucleic acid deglycase DJ-1


Mass: 20071.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q99497, Hydrolases; Acting on ester bonds; Thioester hydrolases, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides, protein deglycase
#2: Chemical ChemComp-8RX / (3~{R})-3-(pent-4-ynylcarbamoyl)pyrrolidine-1-carboximidothioic acid


Mass: 239.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 18.6% (v/v) PEG3350, 170 mM NaNO3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→33.36 Å / Num. obs: 72940 / % possible obs: 99.4 % / Redundancy: 9.6 % / Biso Wilson estimate: 26.77 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.026 / Rrim(I) all: 0.028 / Net I/σ(I): 35.3
Reflection shellResolution: 1.48→1.53 Å / Rmerge(I) obs: 0.912 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3838 / CC1/2: 0.808 / Rrim(I) all: 0.963 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSVERSION Jan 31, 2020 BUILT=20200417data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→33.36 Å / SU ML: 0.1959 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1816 3630 4.98 %
Rwork0.1478 69310 -
obs0.1494 72940 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.2 Å2
Refinement stepCycle: LAST / Resolution: 1.48→33.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1353 0 15 240 1608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01251385
X-RAY DIFFRACTIONf_angle_d1.21481873
X-RAY DIFFRACTIONf_chiral_restr0.1034224
X-RAY DIFFRACTIONf_plane_restr0.0086244
X-RAY DIFFRACTIONf_dihedral_angle_d18.994514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.47751180.46792694X-RAY DIFFRACTION99.5
1.5-1.520.41011250.38032669X-RAY DIFFRACTION99.71
1.52-1.540.33631390.2882706X-RAY DIFFRACTION99.75
1.54-1.560.28341210.2372654X-RAY DIFFRACTION99.75
1.56-1.590.25591610.20232676X-RAY DIFFRACTION99.86
1.59-1.620.19451610.16992643X-RAY DIFFRACTION99.89
1.62-1.640.21371340.13942686X-RAY DIFFRACTION99.89
1.64-1.670.16081390.1332675X-RAY DIFFRACTION99.93
1.67-1.70.19081690.13082626X-RAY DIFFRACTION99.93
1.71-1.740.14561580.1332653X-RAY DIFFRACTION99.93
1.74-1.780.17051700.12342679X-RAY DIFFRACTION100
1.78-1.820.22081200.1362721X-RAY DIFFRACTION100
1.82-1.860.16541430.13822661X-RAY DIFFRACTION99.96
1.86-1.920.17971250.13362683X-RAY DIFFRACTION100
1.92-1.970.18151800.13262662X-RAY DIFFRACTION100
1.97-2.030.16541460.13972631X-RAY DIFFRACTION99.89
2.04-2.110.1571120.12772715X-RAY DIFFRACTION99.93
2.11-2.190.15831510.13032674X-RAY DIFFRACTION99.96
2.19-2.290.17711460.12552690X-RAY DIFFRACTION99.75
2.29-2.410.15581460.1382645X-RAY DIFFRACTION99.82
2.41-2.560.1951250.15212700X-RAY DIFFRACTION99.65
2.56-2.760.20141200.14622668X-RAY DIFFRACTION99.61
2.76-3.040.17441330.15462688X-RAY DIFFRACTION99.37
3.04-3.480.17821320.13962612X-RAY DIFFRACTION98.18
3.48-4.380.1631150.13752668X-RAY DIFFRACTION98.34
4.38-33.360.1921410.1662531X-RAY DIFFRACTION94.48

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