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- PDB-8ppw: Structure of human PARK7 in complex with GK16S -

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Basic information

Entry
Database: PDB / ID: 8ppw
TitleStructure of human PARK7 in complex with GK16S
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 / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / : / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate ...tyrosine 3-monooxygenase activator activity / cellular response to glyoxal / L-dopa decarboxylase activator activity / peptidyl-cysteine deglycation / peptidyl-arginine deglycation / peptidyl-lysine deglycation / protein deglycation, methylglyoxal removal / : / detoxification of hydrogen peroxide / methylglyoxal catabolic process to lactate / guanine deglycation, methylglyoxal 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 pyrroline-5-carboxylate reductase activity / positive regulation of tyrosine 3-monooxygenase activity / positive regulation of L-dopa biosynthetic process / positive regulation of L-dopa decarboxylase activity / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / glyoxalase (glycolic acid-forming) activity / negative regulation of protein K48-linked deubiquitination / negative regulation of ubiquitin-specific protease activity / protein deglycation, glyoxal removal / guanine deglycation, glyoxal removal / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / glyoxal metabolic process / guanine deglycation / positive regulation of NAD(P)H oxidase activity / glycolate biosynthetic process / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / protein deglycase activity / positive regulation of dopamine biosynthetic process / positive regulation of autophagy of mitochondrion / superoxide dismutase copper chaperone activity / positive regulation of acute inflammatory response to antigenic stimulus / oxidoreductase activity, acting on peroxide as acceptor / lactate biosynthetic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / cellular detoxification of aldehyde / positive regulation of superoxide dismutase activity / small protein activating enzyme binding / Hydrolases; Acting on ester bonds; Thioester hydrolases / peroxiredoxin activity / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of ubiquitin-protein transferase activity / detoxification of copper ion / negative regulation of protein acetylation / positive regulation of transcription regulatory region DNA binding / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of androgen receptor activity / membrane hyperpolarization / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / protein deglycosylation / negative regulation of protein sumoylation / negative regulation of protein export from nucleus / regulation of androgen receptor signaling pathway / cupric ion binding / oxygen sensor activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / insulin secretion / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / positive regulation of reactive oxygen species biosynthetic process / dopamine uptake involved in synaptic transmission / nuclear androgen receptor binding / hydrogen peroxide metabolic process / ubiquitin-specific protease binding / cytokine binding / cuprous ion binding / membrane depolarization / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / single fertilization / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of neuron apoptotic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / negative regulation of protein ubiquitination / activation of protein kinase B activity / mitochondrion organization / adult locomotory behavior / SUMOylation of transcription cofactors / negative regulation of protein phosphorylation / regulation of mitochondrial membrane potential / negative regulation of protein binding / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / adherens junction / Late endosomal microautophagy / negative regulation of protein kinase activity / positive regulation of protein-containing complex assembly / mitochondrial intermembrane space / PML body / autophagy / kinase binding
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-86F / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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

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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)20,3252
Polymers20,0711
Non-polymers2531
Water3,909217
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 area8490 Å2
Unit cell
Length a, b, c (Å)66.823, 66.823, 177.590
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-423-

HOH

21A-475-

HOH

31A-503-

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-86F / (3~{S})-1-(iminomethyl)-~{N}-pent-4-ynyl-pyrrolidine-3-carboxamide


Mass: 253.364 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19N3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 22.3% (v/v) PEG3350, 230 mM KNO3

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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: 1.53→35.23 Å / Num. obs: 66541 / % possible obs: 99.1 % / Redundancy: 16 % / Biso Wilson estimate: 27.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.041 / Net I/σ(I): 31.6
Reflection shellResolution: 1.53→1.59 Å / Rmerge(I) obs: 1.416 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 2615 / CC1/2: 0.768 / Rrim(I) all: 1.458

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSVERSION Jan 31, 2020 BUILT=20200417data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→35.23 Å / SU ML: 0.191 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.8967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1821 3335 5.01 %
Rwork0.1642 63206 -
obs0.1651 66541 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.94 Å2
Refinement stepCycle: LAST / Resolution: 1.53→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 15 217 1586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661393
X-RAY DIFFRACTIONf_angle_d0.97261886
X-RAY DIFFRACTIONf_chiral_restr0.0615225
X-RAY DIFFRACTIONf_plane_restr0.0072247
X-RAY DIFFRACTIONf_dihedral_angle_d15.8372518
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.550.37251670.37632615X-RAY DIFFRACTION98.83
1.55-1.580.3421380.29142619X-RAY DIFFRACTION98.68
1.58-1.60.2711280.25882594X-RAY DIFFRACTION98.84
1.6-1.630.2411250.21822679X-RAY DIFFRACTION99.08
1.63-1.650.22241410.19392608X-RAY DIFFRACTION98.96
1.65-1.680.21751400.19152624X-RAY DIFFRACTION99.07
1.68-1.720.2161560.20222615X-RAY DIFFRACTION99.25
1.72-1.750.24871540.22692636X-RAY DIFFRACTION99.22
1.75-1.790.21721410.20732590X-RAY DIFFRACTION99.2
1.79-1.830.26431390.20412613X-RAY DIFFRACTION99.42
1.83-1.880.21121260.18012653X-RAY DIFFRACTION99.5
1.88-1.930.1591280.18072684X-RAY DIFFRACTION99.33
1.93-1.980.18611290.16532633X-RAY DIFFRACTION99.68
1.98-2.050.19841540.17342613X-RAY DIFFRACTION99.64
2.05-2.120.21351350.17452651X-RAY DIFFRACTION99.68
2.12-2.210.17641800.1662605X-RAY DIFFRACTION99.86
2.21-2.310.1961160.1622691X-RAY DIFFRACTION99.65
2.31-2.430.17861370.15552624X-RAY DIFFRACTION99.89
2.43-2.580.15811390.16442658X-RAY DIFFRACTION99.89
2.58-2.780.22391070.16632689X-RAY DIFFRACTION99.93
2.78-3.060.15691360.1712643X-RAY DIFFRACTION99.89
3.06-3.50.17241530.1482620X-RAY DIFFRACTION99.39
3.5-4.410.14461430.13812626X-RAY DIFFRACTION99.32
4.41-35.230.18031230.15122623X-RAY DIFFRACTION98.18
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)
12.327375788080.2932500471020.6540132671192.16242099152-0.2254548173334.8466918191-0.0796619467888-0.01466247129750.238225428759-0.0668419794003-0.0077888315168-0.072553797504-0.6854514812490.01278412440670.09773023382680.234126522402-0.0204040536044-0.0135969931050.1183916214820.004860000205970.202635461243-20.30521.46914.171
24.4332737695-0.8709412568720.0800780686494.03280994752-1.005684494321.88197342644-0.219852377373-0.2914073750510.642111270752-0.302389520569-0.1368914046650.399951203187-1.0216480163-0.6654272014130.3653376314470.3278690227760.0742217329523-0.03209814977760.195820736328-0.01293714484880.247795596788-26.57624.87112.417
32.84653415948-0.761481328355-0.7585936499963.4998163673-0.3373305113171.668582439630.0366156506327-0.05114843653840.646302207375-0.234445753207-0.1096287637850.219547213494-0.870254240997-0.4386258058860.06730410330350.446193752220.093016812456-0.05416787257860.233959635322-0.01174982786960.298940291709-28.61226.65311.773
44.563212867990.886944780323-0.2095628606171.85054709893-0.8203133130360.362167390666-0.0355281681505-0.259039638180.8550764794910.0368219481505-0.140872337226-0.00101786655317-1.13054477766-0.003249830431240.1758913064110.517425936418-0.0534000716352-0.05192359119250.1809740815070.01541531918620.346990175894-16.72328.85710.944
58.91786665672-1.08421502807-0.1997169539218.30133895397-3.63531236026.985440260870.1171398514520.8674164416060.108664836488-1.57559864055-0.07716121745970.599294594127-0.222893014867-0.505558416499-0.07568321757750.4096777244040.0279479457188-0.06465236092870.3104172183010.01616420578660.242770385089-23.51323.574-2.072
61.80153835123-3.98452964675-0.3912278047859.062571287570.9788438765090.09905519226190.3755932672770.791387696950.700874496711-0.742751265624-0.314369033031-0.702807727719-1.289411572870.442620214635-0.008556211846870.824852058176-0.06567007578320.03656415890830.2790946171680.1128242825880.526010397066-15.52635.7043.309
73.007829179861.319509999440.3773855620583.756456002370.1065852913382.02919981975-0.08433386117330.2693850037910.464089063884-0.138355486296-0.124518750365-0.20648977104-0.6536455482260.4222056422470.2102218560120.42521524013-0.1134929891640.003000565666940.2429146447390.08156596558770.281367878011-10.66925.3791.623
83.386799296070.7582033547-0.8631771335145.07909203354-1.567270773882.21180271133-0.02818899667890.3313557402490.12272176929-0.634164766258-0.240392367046-0.544887021313-0.228764973810.6912488134580.2905554179960.344165703595-0.07216389666790.07496337230790.3038119479670.07064738788630.274310918425-6.89719.1050.126
94.266598500113.247915523921.976018176376.948766616463.138186064366.71032486405-0.02722959214-0.1099243953680.156683943253-0.0558665352352-0.027775559824-0.326303287193-0.5273125705340.5334780692830.08036026334480.179563552876-0.0739271626881-0.0082565392730.2134891406060.03700997261370.200168171381-10.10518.67615.526
102.38686125911-0.3613778774381.272436628051.08358472943-0.2542882028216.29516296312-0.207532332549-0.0456296656173-0.0511455131013-0.2877149208230.168007424419-0.156134704105-0.04691761377360.5695299561720.06437381496560.199443823668-0.07169402219170.01346078730310.2185039852740.0188402225240.194260694157-9.5414.48221.043
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:28 )A3 - 28
2X-RAY DIFFRACTION2( CHAIN A AND RESID 29:47 )A29 - 47
3X-RAY DIFFRACTION3( CHAIN A AND RESID 48:64 )A48 - 64
4X-RAY DIFFRACTION4( CHAIN A AND RESID 65:75 )A65 - 75
5X-RAY DIFFRACTION5( CHAIN A AND RESID 76:85 )A76 - 85
6X-RAY DIFFRACTION6( CHAIN A AND RESID 86:97 )A86 - 97
7X-RAY DIFFRACTION7( CHAIN A AND RESID 98:126 )A98 - 126
8X-RAY DIFFRACTION8( CHAIN A AND RESID 127:157 )A127 - 157
9X-RAY DIFFRACTION9( CHAIN A AND RESID 158:173 )A158 - 173
10X-RAY DIFFRACTION10( CHAIN A AND RESID 174:188 )A174 - 188

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