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- PDB-1w6v: Solution structure of the DUSP domain of hUSP15 -

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Basic information

Entry
Database: PDB / ID: 1w6v
TitleSolution structure of the DUSP domain of hUSP15
ComponentsUBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15
KeywordsHYDROLASE / UCH / USP / DUB / DEUBIQUITYLATION / DEUBIQUITINATING ENZYME / UBIQUITIN / UBIQUITIN SPECIFIC PROTEASE / UBIQUITIN CARBOXYTERMINAL HYDROLASE / CLEAVAGE / USP15 / DUB15 / UBP15 / ENDOPEPTIDASE / THIOLESTERASE / DUSP / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS
Function / homology
Function and homology information


regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / deubiquitinase activity / transforming growth factor beta receptor binding / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling ...regulation of intrinsic apoptotic signaling pathway in response to osmotic stress by p53 class mediator / negative regulation of antifungal innate immune response / protein K27-linked deubiquitination / positive regulation of RIG-I signaling pathway / ubiquitin-modified histone reader activity / monoubiquitinated protein deubiquitination / deubiquitinase activity / transforming growth factor beta receptor binding / K48-linked deubiquitinase activity / transcription elongation-coupled chromatin remodeling / protein deubiquitination / SMAD binding / BMP signaling pathway / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / UCH proteinases / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / Ub-specific processing proteases / cysteine-type endopeptidase activity / mitochondrion / proteolysis / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DUSP-like / DUSP-like / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal ...DUSP-like / DUSP-like / Ubiquitin-like domain, USP-type / Ubiquitin-like domain / Peptidase C19, ubiquitin-specific peptidase, DUSP domain / DUSP-like superfamily / DUSP domain / DUSP domain profile. / Domain in ubiquitin-specific proteases. / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / RNA 3'-terminal phosphate cyclase/enolpyruvate transferase, alpha/beta / 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. / Papain-like cysteine peptidase superfamily / Ubiquitin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 15
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CANDID IN CYANA, CNS FOR WATER REFINEMENT
AuthorsDe Jong, R.D. / Ab, E. / Diercks, T. / Truffault, V. / Daniels, M. / Kaptein, R. / Folkers, G.E.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Solution Structure of the Human Ubiquitin-Specific Protease 15 Dusp Domain.
Authors: De Jong, R.N. / Ab, E. / Diercks, T. / Truffault, V. / Daniels, M. / Kaptein, R. / Folkers, G.E.
History
DepositionAug 24, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15


Theoretical massNumber of molelcules
Total (without water)16,1491
Polymers16,1491
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)13 / 20SMALLEST MAXIMUM RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15 / UBIQUITIN THIOLESTERASE 15 / UBIQUITIN-SPECIFIC PROCESSING PROTEASE 15 / UBIQUITINATING ENZYME 15 / ...UBIQUITIN THIOLESTERASE 15 / UBIQUITIN-SPECIFIC PROCESSING PROTEASE 15 / UBIQUITINATING ENZYME 15 / UNPH-2 / UNPH4


Mass: 16149.077 Da / Num. of mol.: 1 / Fragment: DUSP DOMAIN, RESIDUES 1-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: SELF MADE CDNA LIBRARY OF MULTIPLE HUMAN CARCINOMA CELL LINES
Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y4E8, EC: 3.1.2.15
Compound detailsCATALYTIC ACTIVITY: UBIQUITIN C-TERMINAL THIOLESTER + H(2)O = UBIQUITIN + A THIOL.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO
121HN(CA)CO
131HN(CA)CB
141CBCA(CO)NH
151HNCA
161HBHA(CO)NH
171HNCAHA
181CCH-COSY
191(H)CCH-TOCSY
1101HNH-NOESY
1111HCH-NOESY
1121CNH- NOESY
1131HH-NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 15N- AND 13C, 15N-LABELED HIS-TAGGED HUSP15_1-120

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 150 mM / pH: 7.0 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGERrefinement
Sparkystructure solution
RefinementMethod: CANDID IN CYANA, CNS FOR WATER REFINEMENT / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
NMR ensembleConformer selection criteria: SMALLEST MAXIMUM RESTRAINT VIOLATION
Conformers calculated total number: 20 / Conformers submitted total number: 13

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