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- PDB-5xve: Crystal structure of human USP2 C276S mutant in complex with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 5xve
TitleCrystal structure of human USP2 C276S mutant in complex with ubiquitin
Components
  • Ubiquitin carboxyl-terminal hydrolase 2
  • Ubiquitin-40S ribosomal protein S27a
KeywordsHYDROLASE / ubiquitin specific protease for anticancer target
Function / homology
Function and homology information


Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway ...Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Downregulation of ERBB4 signaling / Spry regulation of FGF signaling / Downregulation of ERBB2:ERBB3 signaling / NOD1/2 Signaling Pathway / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / APC-Cdc20 mediated degradation of Nek2A / EGFR downregulation / TCF dependent signaling in response to WNT / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / NF-kB is activated and signals survival / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Senescence-Associated Secretory Phenotype (SASP) / Regulation of innate immune responses to cytosolic DNA / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Regulation of FZD by ubiquitination / PINK1-PRKN Mediated Mitophagy / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / Translesion synthesis by POLK / Translesion synthesis by POLI / Regulation of necroptotic cell death / MAP3K8 (TPL2)-dependent MAPK1/3 activation / HDR through Homologous Recombination (HRR) / Josephin domain DUBs / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in GG-NER / Dual Incision in GG-NER / Fanconi Anemia Pathway / Regulation of TP53 Activity through Phosphorylation / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Negative regulation of MET activity / Cyclin D associated events in G1 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Downregulation of ERBB2 signaling / E3 ubiquitin ligases ubiquitinate target proteins / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / Regulation of expression of SLITs and ROBOs / Interferon alpha/beta signaling / Endosomal Sorting Complex Required For Transport (ESCRT) / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / RAS processing / Pexophagy / Inactivation of CSF3 (G-CSF) signaling / Negative regulation of FLT3 / Regulation of BACH1 activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / Termination of translesion DNA synthesis / Ovarian tumor domain proteases / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Negative regulation of MAPK pathway / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Iron uptake and transport / Deactivation of the beta-catenin transactivating complex / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / DNA Damage Recognition in GG-NER / Activation of NF-kappaB in B cells / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of AXIN / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling
Similarity search - Function
Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / Cathepsin B; Chain A / S27a-like superfamily ...Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / Cysteine proteinases / Cathepsin B; Chain A / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / Papain-like cysteine peptidase superfamily / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 2 / Ubiquitin-ribosomal protein eS31 fusion protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsChou, C.Y. / Tang, H.C.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology105-2320-B-010-012 Taiwan
Ministry of Science and Technology104-2320-B-010-034 Taiwan
CitationJournal: Sci Rep / Year: 2018
Title: 6-Thioguanine is a noncompetitive and slow binding inhibitor of human deubiquitinating protease USP2
Authors: Chuang, S.J. / Cheng, S.C. / Tang, H.C. / Sun, C.Y. / Chou, C.Y.
History
DepositionJun 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 2
B: Ubiquitin-40S ribosomal protein S27a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8363
Polymers49,7702
Non-polymers651
Water6,413356
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, The complex formation of USP2 and Ub was identified by analytical ultracentrifugation.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-4 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.473, 54.011, 74.753
Angle α, β, γ (deg.)90.00, 107.79, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 2 / 41 kDa ubiquitin-specific protease / Deubiquitinating enzyme 2 / Ubiquitin thioesterase 2 / ...41 kDa ubiquitin-specific protease / Deubiquitinating enzyme 2 / Ubiquitin thioesterase 2 / Ubiquitin-specific-processing protease 2


Mass: 41193.594 Da / Num. of mol.: 1 / Fragment: UNP residues 258-605 / Mutation: C276S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP2, UBP41 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: O75604, ubiquitinyl hydrolase 1
#2: Protein Ubiquitin-40S ribosomal protein S27a / Ubiquitin carboxyl extension protein 80


Mass: 8576.831 Da / Num. of mol.: 1 / Fragment: UNP residues 1-76 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P62992
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / 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: 1.98 Å3/Da / Density % sol: 37.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 21% PEG3350, 8% Tacsimate (pH8.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.24→30 Å / Num. obs: 102971 / % possible obs: 98.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 33
Reflection shellResolution: 1.24→1.28 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.241 / Num. unique obs: 14717 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data collection
HKL-2000data processing
PHASERmodel building
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HD5

2hd5


Resolution: 1.24→30 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.051 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.04 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16403 5587 5.2 %RANDOM
Rwork0.14694 ---
obs0.14784 102800 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.025 Å2
Baniso -1Baniso -2Baniso -3
1--0.64 Å2-0 Å20.18 Å2
2--0.31 Å2-0 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.24→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 1 356 3641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0193494
X-RAY DIFFRACTIONr_bond_other_d0.0020.023335
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.964746
X-RAY DIFFRACTIONr_angle_other_deg0.87737687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0195447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.22923.164177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95815646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2651536
X-RAY DIFFRACTIONr_chiral_restr0.0750.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024001
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02861
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_it0.771.3321675
X-RAY DIFFRACTIONr_mcbond_other0.7691.3321674
X-RAY DIFFRACTIONr_mcangle_it1.0132.0032102
X-RAY DIFFRACTIONr_mcangle_other1.0132.0032103
X-RAY DIFFRACTIONr_scbond_it0.9271.5281819
X-RAY DIFFRACTIONr_scbond_other0.9271.5281819
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1352.2282624
X-RAY DIFFRACTIONr_long_range_B_refined2.00311.8264196
X-RAY DIFFRACTIONr_long_range_B_other1.66511.2533992
X-RAY DIFFRACTIONr_rigid_bond_restr1.17336829
X-RAY DIFFRACTIONr_sphericity_free20.77566
X-RAY DIFFRACTIONr_sphericity_bonded5.00357033
LS refinement shellResolution: 1.24→1.307 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.182 815 -
Rwork0.159 14652 -
obs--97.04 %

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