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Basic information

Entry
Database: PDB / ID: 7en4
TitleMulti-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase.
ComponentsUbiquitin carboxyl-terminal hydrolase YUH1
KeywordsHYDROLASE / PROTEIN solution NMR
Function / homology
Function and homology information


UCH proteinases / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ubiquitin recycling / Neddylation / ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / cytoplasm
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site. / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase YUH1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / energy minimization
AuthorsOkada, M. / Tateishi, Y. / Nojiri, E. / Mikawa, T. / Rajesh, S. / Ogasawa, H. / Ueda, T. / Yagi, H. / Kohno, T. / Kigawa, T. ...Okada, M. / Tateishi, Y. / Nojiri, E. / Mikawa, T. / Rajesh, S. / Ogasawa, H. / Ueda, T. / Yagi, H. / Kohno, T. / Kigawa, T. / Shimada, I. / Guentert, P. / Yutaka, I. / Ikeya, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR13M3 Japan
Japan Society for the Promotion of Science (JSPS)JP15K06979, JP17K07312, JP19H05645, JP26102538, JP25120003, JP16H00779, JP15H01645, JP16H00847, JP17H05887,JP19H05773 Japan
CitationJournal: To Be Published
Title: Multi-state structure determination and dynamics analysis elucidate a new ubiquitin-recognition mechanism of yeast ubiquitin C-terminal hydrolase.
Authors: Okada, M. / Tateishi, Y. / Nojiri, E. / Mikawa, T. / Rajesh, S. / Yagi, H. / Ogasawa, H. / Ueda, T. / Shimada, I. / Kohno, T. / Kigawa, T. / Guentert, P. / Yutaka, I. / Ikeya, T.
History
DepositionApr 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase YUH1


Theoretical massNumber of molelcules
Total (without water)26,4051
Polymers26,4051
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13670 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures randomly selected from each of five clusters
RepresentativeModel #1closest the center of the largest cluster

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase YUH1 / UCH / Ubiquitin thioesterase


Mass: 26405.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35127, ubiquitinyl hydrolase 1

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCA
121isotropic13D HN(CO)CA
131isotropic13D CBCA(CO)NH
141isotropic13D CBCANH
151isotropic13D HBHA(CO)NH
1111isotropic13D H(CCO)NH
1101isotropic13D C(CO)NH
191isotropic13D (H)CCH-TOCSY
181isotropic13D 1H-13C NOESY
171anisotropic13D 1H-15N NOESY
161isotropic13D HSQC-NOESY-HSQC
1123isotropic13D H(CCO)NH
1143isotropic13D CCNH
1133isotropic13D C(CO)NH
1163isotropic12D 1H-1H TOCSY
1153isotropic13D 1H-13C NOESY
1173isotropic13D 1H-15N NOESY
1183isotropic13D TROSY-HNCO
1212isotropic2T1 relaxation
1202isotropic2T2 relaxation
1192isotropic2heteronuclear 1H-15N NOE
1232isotropic3T1 relaxation
1222isotropic3T2 relaxation
1242isotropic3heteronuclear 1H-15N NOE
1252isotropic22D 1H-15N HSQC
1271isotropic22D 1H-13C HSQC
1262anisotropic22D 1H-15N IPAP HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution12 mM [U-100% 13C; U-100% 15N; U-50% 2H] ubiquitin hydrolase, 90% H2O/10% D2O2H13C15N_sample90% H2O/10% D2O
solution22 mM [U-100% 15N] ubiquitin hydrolase, 90% H2O/10% D2O15N_sample90% H2O/10% D2O
solution32 mM Ile/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled ubiquitin hydrolase, 90% H2O/10% D2OILVFYW_selective_sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMubiquitin hydrolase[U-100% 13C; U-100% 15N; U-50% 2H]1
2 mMubiquitin hydrolase[U-100% 15N]2
2 mMubiquitin hydrolaseIle/Leu/Val-methyl-selectively 1H/13C-labeled and Phe/Tyr/Trp-aromatic ring-selectively 1H-labeled3
Sample conditionsIonic strength: 100 mM / Label: conditions_1 / pH: 6.0 / Pressure: AMBIENT Pa / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE IIIBrukerAVANCE III7003

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.99.0Guntert, Mumenthaler and Wuthrichstructure calculation
Azara2.8.1Boucherprocessing
CcpNmr Analysis2.5.0CCPNchemical shift assignment
TopSpin3.5Bruker Biospincollection
OPAL1.4Luginbuhl, Guntert, Billeter and Wuthrichrefinement
CcpNmr Analysis2.5.0CCPNpeak picking
RefinementMethod: energy minimization / Software ordinal: 5
NMR representativeSelection criteria: closest the center of the largest cluster
NMR ensembleConformer selection criteria: structures randomly selected from each of five clusters
Conformers calculated total number: 20 / Conformers submitted total number: 20

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