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- PDB-3tmp: The catalytic domain of human deubiquitinase DUBA in complex with... -

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Basic information

Entry
Database: PDB / ID: 3tmp
TitleThe catalytic domain of human deubiquitinase DUBA in complex with ubiquitin aldehyde
Components
  • OTU domain-containing protein 5
  • Polyubiquitin-C
KeywordsHydrolase/Protein Binding / OTU fold / Deubiquitinase / phosphorylation / Hydrolase-Protein Binding complex
Function / homology
Function and homology information


positive regulation of TORC2 signaling / deubiquitinase activity / protein K48-linked deubiquitination / protein K63-linked deubiquitination / neural crest cell differentiation / K48-linked deubiquitinase activity / negative regulation of type I interferon production / K63-linked deubiquitinase activity / protein deubiquitination / Maturation of protein E ...positive regulation of TORC2 signaling / deubiquitinase activity / protein K48-linked deubiquitination / protein K63-linked deubiquitination / neural crest cell differentiation / K48-linked deubiquitinase activity / negative regulation of type I interferon production / K63-linked deubiquitinase activity / protein deubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / positive regulation of TORC1 signaling / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / InlA-mediated entry of Listeria monocytogenes into host cells / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / NIK-->noncanonical NF-kB signaling / Regulation of NF-kappa B signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / activated TAK1 mediates p38 MAPK activation / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Deactivation of the beta-catenin transactivating complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of signaling by CBL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Fanconi Anemia Pathway / Hh mutants are degraded by ERAD / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Recognition of DNA damage by PCNA-containing replication complex / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / Negative regulation of FGFR2 signaling / Defective CFTR causes cystic fibrosis / Termination of translesion DNA synthesis / Hedgehog ligand biogenesis
Similarity search - Function
Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain ...Cathepsin B; Chain A - #80 / OTU-like cysteine protease / OTU domain / OTU domain profile. / Cathepsin B; Chain A / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin-C / OTU domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsMa, X. / Yin, J. / Hymowitz, S. / Starovasnik, M. / Cochran, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Phosphorylation-dependent activity of the deubiquitinase DUBA.
Authors: Huang, O.W. / Ma, X. / Yin, J. / Flinders, J. / Maurer, T. / Kayagaki, N. / Phung, Q. / Bosanac, I. / Arnott, D. / Dixit, V.M. / Hymowitz, S.G. / Starovasnik, M.A. / Cochran, A.G.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 29, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OTU domain-containing protein 5
B: Polyubiquitin-C
C: OTU domain-containing protein 5
D: Polyubiquitin-C
E: OTU domain-containing protein 5
F: Polyubiquitin-C
G: OTU domain-containing protein 5
H: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)119,2698
Polymers119,2698
Non-polymers00
Water15,241846
1
A: OTU domain-containing protein 5
B: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)29,8172
Polymers29,8172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-6 kcal/mol
Surface area11990 Å2
MethodPISA
2
C: OTU domain-containing protein 5
D: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)29,8172
Polymers29,8172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-7 kcal/mol
Surface area11750 Å2
MethodPISA
3
E: OTU domain-containing protein 5
F: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)29,8172
Polymers29,8172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-5 kcal/mol
Surface area11750 Å2
MethodPISA
4
G: OTU domain-containing protein 5
H: Polyubiquitin-C


Theoretical massNumber of molelcules
Total (without water)29,8172
Polymers29,8172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-6 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.532, 65.296, 65.843
Angle α, β, γ (deg.)90.26, 93.53, 99.28
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
OTU domain-containing protein 5 / Deubiquitinating enzyme A / DUBA


Mass: 21256.529 Da / Num. of mol.: 4 / Fragment: catalytic or OTU domain (Residues 172-351) / Mutation: S172 phosphorylated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUBA, OTUD5 / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q96G74, ubiquitinyl hydrolase 1
#2: Protein
Polyubiquitin-C / Ubiquitin


Mass: 8560.831 Da / Num. of mol.: 4 / Fragment: Ubiquitin-like 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC, ubiquitin aldehyde / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG48
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 20% PEG3350, 0.2 M Ammonium Fluoride, and 0.1M Bis-Tris, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 16, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.91→50 Å / Num. all: 75788 / Num. obs: 73969 / % possible obs: 97.6 % / Redundancy: 2 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.321 / Net I/σ(I): 14.5
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 7278 / Rsym value: 0.321 / % possible all: 95.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→46.35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.345 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22721 3749 5.1 %RANDOM
Rwork0.18987 ---
obs0.19182 70216 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.269 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0.4 Å20.32 Å2
2---0.77 Å2-0.31 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.91→46.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7820 0 0 846 8666
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227969
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9410730
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1125944
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85124.796442
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02815.0421433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1511551
X-RAY DIFFRACTIONr_chiral_restr0.0980.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0216107
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5421.54768
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.54627683
X-RAY DIFFRACTIONr_scbond_it4.04233201
X-RAY DIFFRACTIONr_scangle_it5.944.53047
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 283 -
Rwork0.263 4992 -
obs--94.55 %

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