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- PDB-2muu: The Proteolytic Activity of Ubiquitin-specific Protease 28 Is Mod... -

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Basic information

Entry
Database: PDB / ID: 2muu
TitleThe Proteolytic Activity of Ubiquitin-specific Protease 28 Is Modulated by the N-terminal Domain
ComponentsUbiquitin carboxyl-terminal hydrolase 28
KeywordsHYDROLASE
Function / homology
Function and homology information


protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / response to ionizing radiation / protein deubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity ...protein deubiquitination involved in ubiquitin-dependent protein catabolic process / deubiquitinase activity / response to ionizing radiation / protein deubiquitination / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / DNA damage checkpoint signaling / regulation of protein stability / cellular response to UV / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cell population proliferation / Ub-specific processing proteases / nuclear body / DNA repair / DNA damage response / protein-containing complex / nucleoplasm / nucleus / cytosol
Similarity search - Function
: / Ubiquitin-specific protease UIM domain / : / UBA-like domain / : / 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 UIM domain / : / UBA-like domain / : / 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. / UBA-like superfamily / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
Model detailslowest energy, model1
AuthorsWen, Y. / Shi, L. / Zhang, N.
CitationJournal: Biochem.J. / Year: 2015
Title: The N-terminal ubiquitin-binding region of ubiquitin-specific protease 28 modulates its deubiquitination function: NMR structural and mechanistic insights.
Authors: Wen, Y. / Shi, L. / Ding, Y. / Cui, R. / He, W.T. / Hu, H.Y. / Zhang, N.
History
DepositionSep 17, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase 28


Theoretical massNumber of molelcules
Total (without water)14,5631
Polymers14,5631
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase 28 / Deubiquitinating enzyme 28 / Ubiquitin thioesterase 28 / Ubiquitin-specific-processing protease 28


Mass: 14562.968 Da / Num. of mol.: 1 / Fragment: N-terminal Domain (UNP residues 1-120)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: USP28, KIAA1515 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96RU2, ubiquitinyl hydrolase 1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1232D 1H-13C HSQC
1323D C(CO)NH
1423D HNCO
1523D HNCA
1623D HN(CA)CB
1723D HBHA(CO)NH
1823D HN(CO)CA
1923D H(CCO)NH
11023D HN(CA)CO
11133D (H)CCH-TOCSY
11213D 1H-15N NOESY
11333D 1H-13C NOESY aliphatic

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Sample preparation

Details
Solution-IDContentsSolvent system
110 % D20, 90 % H20, 0.8-1.0 mM [U-15N] USP, 20 mM Na2HPO4/NaH2PO4, 100 mM NaCl, 2 mM DTT, 0.02 % NaNH3, 90% H2O/10% D2O90% H2O/10% D2O
210 % D20, 90 % H20, 0.8-1.0 mM [U-15N; U-13C] USP, 20 mM Na2HPO4/NaH2PO4, 100 mM NaCl, 2 mM DTT, 0.02 % NaNH3, 90% H2O/10% D2O90% H2O/10% D2O
3100 % D20, 0.8-1.0 mM [U-15N; U-13C] USP, 20 mM Na2HPO4/NaH2PO4, 100 mM NaCl, 2 mM DTT, 0.02 % NaNH3, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
10 %D20-11
90 %H20-21
mMUSP-28-3[U-15N]0.8-1.01
20 mMNa2HPO4/NaH2PO4-41
100 mMNaCl-51
2 mMDTT-61
0.02 %NaNH3-71
10 %D20-82
90 %H20-92
mMUSP-28-10[U-15N; U-13C]0.8-1.02
20 mMNa2HPO4/NaH2PO4-112
100 mMNaCl-122
2 mMDTT-132
0.02 %NaNH3-142
100 %D20-153
mMUSP-28-16[U-15N; U-13C]0.8-1.03
20 mMNa2HPO4/NaH2PO4-173
100 mMNaCl-183
2 mMDTT-193
0.02 %NaNH3-203
Sample conditionsIonic strength: 0.15 / pH: 6.5 / Pressure: 1 atm / Temperature: 298.2 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH2.34Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.34Schwieters, Kuszewski, Tjandra and Clorerefinement
NMR constraintsNOE constraints total: 1548 / NOE intraresidue total count: 648 / NOE long range total count: 115 / NOE medium range total count: 271 / NOE sequential total count: 514 / Hydrogen bond constraints total count: 58
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 14

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