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- PDB-4ogf: Crystal Structure of Human DJ-1 with glyoxylate as substrate analog -

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Basic information

Entry
Database: PDB / ID: 4ogf
TitleCrystal Structure of Human DJ-1 with glyoxylate as substrate analog
ComponentsProtein DJ-1
KeywordsLYASE / Glyoxalase
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 (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Parkinson disease protein 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChoi, D. / Kim, J. / Ryu, K.-S. / Park, C.
CitationJournal: Febs J. / Year: 2014
Title: Stereospecific mechanism of DJ-1 glyoxalases inferred from their hemithioacetal-containing crystal structures.
Authors: Choi, D. / Kim, J. / Ha, S. / Kwon, K. / Kim, E.H. / Lee, H.Y. / Ryu, K.S. / Park, C.
History
DepositionJan 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein DJ-1


Theoretical massNumber of molelcules
Total (without water)19,7451
Polymers19,7451
Non-polymers00
Water2,288127
1
A: Protein DJ-1

A: Protein DJ-1


Theoretical massNumber of molelcules
Total (without water)39,4902
Polymers39,4902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-2/31
Buried area2670 Å2
ΔGint-20 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.692, 74.692, 74.937
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Protein DJ-1 / Oncogene DJ1 / Parkinson disease protein 7


Mass: 19744.805 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, D-lactate dehydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 1.4 M sodium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 32086 / % possible obs: 99.1 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.047 / Χ2: 1.098 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.664.40.39231040.569197.4
1.66-1.724.90.34931220.658198.3
1.72-1.85.50.29331730.763199
1.8-1.96.20.22431660.875199.1
1.9-2.027.10.16632061.001199.4
2.02-2.1780.11131941.112199.6
2.17-2.398.60.07832101.154199.4
2.39-2.749.20.05832281.165199.8
2.74-3.459.90.04732771.709199.8
3.45-50100.02834061.106199.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PDV

1pdv


Resolution: 1.6→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2347 3205 6.7 %
Rwork0.212 28859 -
obs-32064 99.119 %
Solvent computationBsol: 43.4915 Å2
Displacement parametersBiso max: 79.5 Å2 / Biso mean: 27.1511 Å2 / Biso min: 17.43 Å2
Baniso -1Baniso -2Baniso -3
1-2.854 Å20 Å20 Å2
2--2.854 Å20 Å2
3----5.708 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 0 127 1508
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.281
X-RAY DIFFRACTIONc_mcbond_it1.1421.5
X-RAY DIFFRACTIONc_scbond_it2.2462
X-RAY DIFFRACTIONc_mcangle_it1.7332
X-RAY DIFFRACTIONc_scangle_it3.2392.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.660.39123410.39872917325868.6
1.66-1.760.33794980.32954177467598.5
1.76-1.90.26184820.23474247472999
1.9-2.090.23214790.20084291477099.6
2.09-2.390.21244680.18154314478299.4
2.39-3.020.24154700.22194368483899.8
3.02-500.20484670.18664545501299.7
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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