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- PDB-6af9: DJ-1 with isatin bound (high concentration) -

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Basic information

Entry
Database: PDB / ID: 6af9
TitleDJ-1 with isatin bound (high concentration)
ComponentsProtein/nucleic acid deglycase DJ-1
KeywordsHYDROLASE / DJ-1 / Parkinson's disease / Drug discovery / Fragment-based drug discovery
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 / glutathione deglycation / 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 / glutathione deglycation / 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 / glycolate biosynthetic process / guanine deglycation, glyoxal removal / glyoxal metabolic process / negative regulation of nitrosative stress-induced intrinsic apoptotic signaling pathway / detection of oxidative stress / guanine deglycation / detoxification of mercury ion / protein deglycase / methylglyoxal metabolic process / positive regulation of mitochondrial electron transport, NADH to ubiquinone / mercury ion binding / oxidoreductase activity, acting on peroxide as acceptor / protein deglycase activity / positive regulation of acute inflammatory response to antigenic stimulus / positive regulation of dopamine biosynthetic process / superoxide dismutase copper chaperone activity / positive regulation of NAD(P)H oxidase activity / positive regulation of autophagy of mitochondrion / 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 / regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of ubiquitin-protein transferase activity / peroxiredoxin activity / detoxification of copper ion / negative regulation of protein acetylation / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / 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 / protein deglycosylation / negative regulation of protein sumoylation / oxygen sensor activity / regulation of androgen receptor signaling pathway / negative regulation of protein export from nucleus / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / cupric ion binding / ubiquitin-like protein conjugating enzyme binding / insulin secretion / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / dopamine uptake involved in synaptic transmission / positive regulation of reactive oxygen species biosynthetic process / nuclear androgen receptor binding / hydrogen peroxide metabolic process / ubiquitin-specific protease binding / cytokine binding / cuprous ion binding / single fertilization / membrane depolarization / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / 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 / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / negative regulation of protein binding / positive regulation of interleukin-8 production / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein-containing complex assembly / adherens junction / Late endosomal microautophagy / negative regulation of protein kinase activity / mitochondrial intermembrane space / PML body / cellular response to hydrogen peroxide / autophagy
Similarity search - Function
Protein/nucleic acid deglycase DJ-1 / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ISATIN / Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsCaaveiro, J.M.M. / Tashiro, S. / Tsumoto, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)Platform for Drug Discovery, Informatics and Structural Life Science Japan
Japan Society for the Promotion of Science25249115 Japan
Japan Society for the Promotion of Science16H02420 Japan
Japan Society for the Promotion of Science15K06962 Japan
Citation
Journal: ACS Chem. Biol. / Year: 2018
Title: Discovery and Optimization of Inhibitors of the Parkinson's Disease Associated Protein DJ-1.
Authors: Tashiro, S. / Caaveiro, J.M.M. / Nakakido, M. / Tanabe, A. / Nagatoishi, S. / Tamura, Y. / Matsuda, N. / Liu, D. / Hoang, Q.Q. / Tsumoto, K.
#1: Journal: Biochemistry / Year: 2014
Title: Thermodynamic and structural characterization of the specific binding of Zn(II) to human protein DJ-1.
Authors: Tashiro, S. / Caaveiro, J.M.M. / Wu, C.X. / Hoang, Q.Q. / Tsumoto, K.
History
DepositionAug 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein/nucleic acid deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3945
Polymers19,9171
Non-polymers4774
Water3,909217
1
A: Protein/nucleic acid deglycase DJ-1
hetero molecules

A: Protein/nucleic acid deglycase DJ-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,78810
Polymers39,8342
Non-polymers9548
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area5120 Å2
ΔGint2 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.100, 75.100, 75.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 19917.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PARK7 / Plasmid: pET28B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
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-ISN / ISATIN / Isatin


Mass: 147.131 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H5NO2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsThere are two reaction forms of ISN in this structure. ISN201 is bonded with Cys106 through a ...There are two reaction forms of ISN in this structure. ISN201 is bonded with Cys106 through a double bond opening, and ISN202/203 are bonded to Lys148/182 respectively through Schiff base.

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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: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100mM TRIS-HCl, 200mM sodium citrate, 30% PEG 400, 5mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.39→29.9 Å / Num. obs: 48912 / % possible obs: 98.3 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.6
Reflection shellResolution: 1.39→1.47 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2.4 / % possible all: 89.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLM7.0.9data reduction
SCALA3.3.20data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SOA

1soa


Resolution: 1.39→29.9 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.207 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.036 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13476 1517 3.1 %RANDOM
Rwork0.11343 ---
obs0.11408 47361 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.265 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.39→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1376 0 32 217 1625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0191486
X-RAY DIFFRACTIONr_bond_other_d0.0010.021508
X-RAY DIFFRACTIONr_angle_refined_deg2.052.0222009
X-RAY DIFFRACTIONr_angle_other_deg0.9273.0013495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3955201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.23425.4951
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.40315280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.293157
X-RAY DIFFRACTIONr_chiral_restr0.1230.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211659
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02291
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0921.467763
X-RAY DIFFRACTIONr_mcbond_other1.91.46762
X-RAY DIFFRACTIONr_mcangle_it2.3792.206956
X-RAY DIFFRACTIONr_mcangle_other2.3962.211957
X-RAY DIFFRACTIONr_scbond_it5.3731.973723
X-RAY DIFFRACTIONr_scbond_other5.3711.975724
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7282.7551046
X-RAY DIFFRACTIONr_long_range_B_refined5.54214.5961849
X-RAY DIFFRACTIONr_long_range_B_other4.95113.3551735
X-RAY DIFFRACTIONr_rigid_bond_restr3.82432993
X-RAY DIFFRACTIONr_sphericity_free37.244582
X-RAY DIFFRACTIONr_sphericity_bonded13.24953103
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 99 -
Rwork0.248 2974 -
obs--85.29 %

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