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- PDB-6oam: Crystal Structure of ChlaDUB2 DUB domain -

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Basic information

Entry
Database: PDB / ID: 6oam
TitleCrystal Structure of ChlaDUB2 DUB domain
Components
  • Deubiquitinase and deneddylase Dub2
  • Ubiquitin
KeywordsHYDROLASE/PROTEIN TRANSPORT / Chlamydia / Inclusion / Membrane / HYDROLASE / HYDROLASE-PROTEIN TRANSPORT complex
Function / homology
Function and homology information


deNEDDylase activity / protein deneddylation / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I ...deNEDDylase activity / protein deneddylation / hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein deubiquitination / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / VLDLR internalisation and degradation / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / positive regulation of protein ubiquitination / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Gap-filling DNA repair synthesis and ligation in GG-NER / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / activated TAK1 mediates p38 MAPK activation / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / TNFR2 non-canonical NF-kB pathway / Regulation of signaling by CBL / AUF1 (hnRNP D0) binds and destabilizes mRNA / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Fanconi Anemia Pathway / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A
Similarity search - Function
Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / 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 ...Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / 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
Similarity search - Domain/homology
Deubiquitinase and deneddylase Dub2 / Ubiquitin B / Polyubiquitin-B
Similarity search - Component
Biological speciesChlamydia trachomatis serovar L2 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsHausman, J.M. / Das, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)2R01GM103401 United States
CitationJournal: Biochemistry / Year: 2020
Title: The Two Deubiquitinating Enzymes fromChlamydia trachomatisHave Distinct Ubiquitin Recognition Properties.
Authors: Hausman, J.M. / Kenny, S. / Iyer, S. / Babar, A. / Qiu, J. / Fu, J. / Luo, Z.Q. / Das, C.
History
DepositionMar 17, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deubiquitinase and deneddylase Dub2
D: Ubiquitin
B: Deubiquitinase and deneddylase Dub2
C: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)74,3234
Polymers74,3234
Non-polymers00
Water00
1
A: Deubiquitinase and deneddylase Dub2
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)37,1612
Polymers37,1612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-11 kcal/mol
Surface area14700 Å2
MethodPISA
2
B: Deubiquitinase and deneddylase Dub2
C: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)37,1612
Polymers37,1612
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-11 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.692, 108.692, 62.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Deubiquitinase and deneddylase Dub2 / ChlaDub2


Mass: 28602.465 Da / Num. of mol.: 2 / Fragment: residues 88-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis serovar L2 (strain 434/Bu / ATCC VR-902B) (bacteria)
Strain: 434/Bu / ATCC VR-902B / Gene: cdu2, CTL0246 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: B0B999, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Ubiquitin


Mass: 8558.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pGEX-6P-1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: J3QS39, UniProt: P0CG47*PLUS
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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES sodium pH 7.5, 0.8 M sodium phosphate monobasic monohydrate, 0.8 M sodium phosphate monobasic, 0.1M Cesium chloride

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→48.61 Å / Num. obs: 25243 / % possible obs: 99.78 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Net I/σ(I): 22.22
Reflection shellResolution: 2.5→2.61 Å / Num. unique obs: 3083

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MRN,1UBQ

6mrn

1ubq


Resolution: 2.503→48.609 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 33.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3057 1281 5.07 %
Rwork0.2832 --
obs0.2843 25243 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.503→48.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5019 0 0 0 5019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.025119
X-RAY DIFFRACTIONf_angle_d2.4426942
X-RAY DIFFRACTIONf_dihedral_angle_d19.7023118
X-RAY DIFFRACTIONf_chiral_restr0.106782
X-RAY DIFFRACTIONf_plane_restr0.014894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5033-2.60350.33841620.27582628X-RAY DIFFRACTION99
2.6035-2.7220.29361390.29342644X-RAY DIFFRACTION100
2.722-2.86540.29961260.30612654X-RAY DIFFRACTION100
2.8654-3.04490.38961120.33492668X-RAY DIFFRACTION100
3.0449-3.280.34481530.33062658X-RAY DIFFRACTION100
3.28-3.610.36921660.3262628X-RAY DIFFRACTION100
3.61-4.13210.33161360.2942692X-RAY DIFFRACTION100
4.1321-5.20510.26931470.25752681X-RAY DIFFRACTION100
5.2051-48.61770.25951400.24942709X-RAY DIFFRACTION99

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