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- PDB-3a7s: Catalytic domain of UCH37 -

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Basic information

Entry
Database: PDB / ID: 3a7s
TitleCatalytic domain of UCH37
ComponentsUbiquitin carboxyl-terminal hydrolase isozyme L5
KeywordsHYDROLASE / ubiquitin-proteasome pathway / Alternative splicing / Polymorphism / Protease / Proteasome / Thiol protease / Ubl conjugation pathway
Function / homology
Function and homology information


lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / cytosolic proteasome complex / Ino80 complex / positive regulation of smoothened signaling pathway / midbrain development / endopeptidase inhibitor activity / proteasome binding ...lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / cytosolic proteasome complex / Ino80 complex / positive regulation of smoothened signaling pathway / midbrain development / endopeptidase inhibitor activity / proteasome binding / regulation of chromosome organization / regulation of DNA replication / regulation of embryonic development / protein deubiquitination / regulation of DNA repair / regulation of proteasomal protein catabolic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / telomere maintenance / positive regulation of DNA repair / Downregulation of TGF-beta receptor signaling / UCH proteinases / ubiquitin-dependent protein catabolic process / DNA recombination / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / regulation of cell cycle / chromatin remodeling / DNA repair / nucleolus / positive regulation of DNA-templated transcription / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily ...Ubiquitinyl hydrolase, UCH37 type / Ubiquitinyl hydrolase-L5 / Peptidase C12, C-terminal domain / Ubiquitin carboxyl-terminal hydrolases / Ubiquitin C-terminal Hydrolase UCH-l3 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Peptidase C12, ubiquitin carboxyl-terminal hydrolase superfamily / Ubiquitin carboxyl-terminal hydrolase, family 1 / Peptidase C12, ubiquitin carboxyl-terminal hydrolase / Papain-like cysteine peptidase superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase isozyme L5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsNishio, K. / Kim, S.W. / Kawai, K. / Mizushima, T. / Yamane, T. / Hamazaki, J. / Murata, S. / Tanaka, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Crystal structure of the de-ubiquitinating enzyme UCH37 (human UCH-L5) catalytic domain
Authors: Nishio, K. / Kim, S.W. / Kawai, K. / Mizushima, T. / Yamane, T. / Hamazaki, J. / Murata, S. / Tanaka, K. / Morimoto, Y.
History
DepositionOct 4, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7032
Polymers25,6681
Non-polymers351
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules

A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4074
Polymers51,3362
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1350 Å2
ΔGint-11 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.583, 57.064, 48.736
Angle α, β, γ (deg.)90.00, 100.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ubiquitin carboxyl-terminal hydrolase isozyme L5 / UCH-L5 / Ubiquitin thioesterase L5 / Ubiquitin C-terminal hydrolase UCH37


Mass: 25667.932 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, UNP residues 1-228 / Mutation: C88A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UCH37 / Plasmid: pGEX-6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Y5K5, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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

Crystal
ID
1
2
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 22% PEG 4000, 0.2M Magnesium chloride, 0.1M Tris-HCl, 3.5% Xylitol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11002
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL44XU10.9
SYNCHROTRONSPring-8 BL44XU20.97914, 0.97946, 0.96422
Detector
TypeIDDetectorDateDetails
Bruker DIP-60401CCDMay 22, 2008mirrors
Bruker DIP-60402CCDFeb 17, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double-crystalSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.979141
30.979461
40.964221
ReflectionResolution: 2.2→50 Å / Num. all: 9366 / Num. obs: 9161 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.36
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.409 / Num. unique all: 880 / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX2.13model building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX2.13phasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→19.93 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1328807.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 471 5.2 %RANDOM
Rwork0.205 ---
all-9308 --
obs-9089 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.8346 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 57.2 Å2
Baniso -1Baniso -2Baniso -3
1--13.02 Å20 Å2-1.11 Å2
2--0.55 Å20 Å2
3---12.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1615 0 1 10 1626
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.94
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 74 5.1 %
Rwork0.27 1387 -
obs-1461 95.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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