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- PDB-3rii: Crystal structure of the catalytic domain of UCHL5, a proteasome-... -

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Basic information

Entry
Database: PDB / ID: 3rii
TitleCrystal structure of the catalytic domain of UCHL5, a proteasome-associated human deubiquitinating enzyme, reveals an unproductive form of the enzyme
ComponentsUbiquitin carboxyl-terminal hydrolase isozyme L5
KeywordsHYDROLASE / alpha-beta-alpha fold / Thiol hydroalse / Cysteine protease / deubiquitinating enzyme / ubiquitin hydrolase
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 / MOLECULAR REPLACEMENT / Resolution: 2.0008 Å
AuthorsDas, C.
CitationJournal: Febs J. / Year: 2011
Title: Crystal structure of the catalytic domain of UCHL5, a proteasome-associated human deubiquitinating enzyme, reveals an unproductive form of the enzyme.
Authors: Maiti, T.K. / Permaul, M. / Boudreaux, D.A. / Mahanic, C. / Mauney, S. / Das, C.
History
DepositionApr 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2011Group: Structure summary
Revision 1.2Dec 14, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,8085
Polymers52,6602
Non-polymers1483
Water5,008278
1
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4163
Polymers26,3301
Non-polymers862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3922
Polymers26,3301
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules

B: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8085
Polymers52,6602
Non-polymers1483
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1750 Å2
ΔGint-10 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.395, 99.034, 48.145
Angle α, β, γ (deg.)90.00, 96.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 26329.861 Da / Num. of mol.: 2 / Fragment: Catalytic domain (UNP Residues 1-228) / Mutation: C88S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AD-019, CGI-70, UCH37, UCHL5 / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9Y5K5, ubiquitinyl hydrolase 1
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG 3350, 0.1M MgCl2, 0.1M Tris-HCl, pH 8.5, 3% Trimethyl amino oxide, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97948 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 27, 2008 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 27641 / Num. obs: 27641 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 12.9
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2641 / Rsym value: 0.462 / % possible all: 93.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.0008→41.054 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1395 5.1 %Random
Rwork0.1751 ---
obs0.1774 27355 95.8 %-
all-27641 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.995 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7491 Å2-0 Å2-0.6562 Å2
2---1.0989 Å20 Å2
3----0.6502 Å2
Refinement stepCycle: LAST / Resolution: 2.0008→41.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 9 278 3628
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033427
X-RAY DIFFRACTIONf_angle_d0.6584635
X-RAY DIFFRACTIONf_dihedral_angle_d15.9531235
X-RAY DIFFRACTIONf_chiral_restr0.046507
X-RAY DIFFRACTIONf_plane_restr0.002607
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.0008-2.07240.29411460.22792449264191
2.0724-2.15530.26871580.20452507270494
2.1553-2.25340.24711400.17832533270594
2.2534-2.37220.22951240.17822524269294
2.3722-2.52080.24081210.17622561273993
2.5208-2.71540.24281410.18452591277196
2.7154-2.98860.23341420.17382655280898
2.9886-3.42090.21821470.16492685284299
3.4209-4.30920.19351490.150427092860100
4.3092-41.06260.20171270.18132746287999
Refinement TLS params.Method: refined / Origin x: -10.1824 Å / Origin y: -28.5587 Å / Origin z: -12.5762 Å
111213212223313233
T0.1287 Å20.0061 Å20.0177 Å2-0.1008 Å20.0253 Å2--0.1345 Å2
L1.5815 °20.3343 °20.7341 °2-0.3109 °20.2557 °2--0.9451 °2
S-0.0012 Å °0.0023 Å °-0.0337 Å °-0.0206 Å °0.0294 Å °-0.0269 Å °-0.0129 Å °0.0479 Å °-0.0258 Å °
Refinement TLS groupSelection details: all

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