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

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Basic information

Entry
Database: PDB / ID: 3ris
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 / cysteine protease / thiol hydrolase / 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 / Ino80 complex / cytosolic proteasome complex / positive regulation of smoothened signaling pathway / midbrain development / regulation of chromosome organization / endopeptidase inhibitor activity ...lateral ventricle development / regulation of DNA strand elongation / positive regulation of telomere maintenance in response to DNA damage / forebrain morphogenesis / Ino80 complex / cytosolic proteasome complex / positive regulation of smoothened signaling pathway / midbrain development / regulation of chromosome organization / endopeptidase inhibitor activity / proteasome binding / protein deubiquitination / regulation of DNA replication / regulation of embryonic development / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / regulation of DNA repair / regulation of proteasomal protein catabolic process / positive regulation of DNA repair / telomere maintenance / 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: 2.398 Å
AuthorsDas, C. / Permaul, M. / Maiti, T.K.
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 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,8498
Polymers110,4694
Non-polymers3804
Water4,017223
1
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7132
Polymers27,6171
Non-polymers961
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)27,8053
Polymers27,6171
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ubiquitin carboxyl-terminal hydrolase isozyme L5


Theoretical massNumber of molelcules
Total (without water)27,6171
Polymers27,6171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7132
Polymers27,6171
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Ubiquitin carboxyl-terminal hydrolase isozyme L5
C: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3313
Polymers55,2342
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-27 kcal/mol
Surface area22200 Å2
MethodPISA
6
B: Ubiquitin carboxyl-terminal hydrolase isozyme L5
D: Ubiquitin carboxyl-terminal hydrolase isozyme L5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5195
Polymers55,2342
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-43 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.393, 41.670, 138.729
Angle α, β, γ (deg.)90.00, 89.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 7 - 238 / Label seq-ID: 12 - 243

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

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


Mass: 27617.236 Da / Num. of mol.: 4 / Fragment: Catalytic domain (UNP Residues 1-140)
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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.6 M Ammonium sulfate, 0.1 M Tris-HCl, pH 8.5, 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: 1.03303 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2008 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03303 Å / Relative weight: 1
ReflectionResolution: 2.398→50 Å / Num. all: 39644 / Num. obs: 39644 / % possible obs: 99.1 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6 / Redundancy: 3.5 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 14.7
Reflection shellResolution: 2.398→2.49 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.648 / Mean I/σ(I) obs: 1.6 / Num. unique all: 3691 / Rsym value: 0.648 / % possible all: 92.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.398→41.7 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 22.266 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25827 1987 5 %RANDOM
Rwork0.20107 ---
all0.20403 39644 --
obs0.20403 37595 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.041 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.13 Å2
2--0.02 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.398→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7190 0 21 223 7434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227378
X-RAY DIFFRACTIONr_bond_other_d00.0210
X-RAY DIFFRACTIONr_angle_refined_deg1.0451.9469963
X-RAY DIFFRACTIONr_angle_other_deg12.04320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7925894
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40724.801377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.616151272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2231540
X-RAY DIFFRACTIONr_chiral_restr0.1110.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025640
X-RAY DIFFRACTIONr_nbd_refined0.1850.23043
X-RAY DIFFRACTIONr_nbd_other0.1710.23
X-RAY DIFFRACTIONr_nbtor_refined0.3020.25008
X-RAY DIFFRACTIONr_nbtor_other0.2530.25
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.2109
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.28
X-RAY DIFFRACTIONr_mcbond_it1.8271.54603
X-RAY DIFFRACTIONr_mcangle_it3.27727191
X-RAY DIFFRACTIONr_scbond_it2.57933146
X-RAY DIFFRACTIONr_scangle_it4.434.52769
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A887medium positional0.440.5
2B887medium positional0.450.5
3C887medium positional0.570.5
4D887medium positional0.460.5
1A890loose positional0.95
2B890loose positional0.945
3C890loose positional1.095
4D890loose positional1.075
1A887medium thermal2.372
2B887medium thermal2.362
3C887medium thermal2.242
4D887medium thermal2.492
1A890loose thermal5.2110
2B890loose thermal5.1210
3C890loose thermal4.8510
4D890loose thermal5.6110
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 136 -
Rwork0.294 2502 -
obs-3691 88.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2919-0.67530.03420.41380.20690.8308-0.01420.0661-0.01440.03250.0433-0.09810.0139-0.0262-0.02910.0068-0.02610.00350.113-0.00260.0919-10.01-2.29157.355
20.7128-0.09640.06610.6586-0.03010.0068-0.00440.17730.0735-0.01870.0027-0.0216-0.0061-0.11020.00170.0239-0.0052-0.00330.21350.00140.0364-19.1495.25651.706
32.3494-0.9285-0.71290.6808-0.08630.6478-0.1279-0.03020.05720.03350.157-0.157-0.0363-0.1022-0.02910.0279-0.00040.01840.1293-0.00470.0394-12.093-0.18961.192
41.6901-0.46980.45630.49450.10882.0573-0.0869-0.00660.1046-0.02650.0503-0.37010.01410.2820.0367-0.0615-0.00270.04610.1211-0.00540.11210.766-1.00755.603
51.85870.56321.91431.47571.2952.3631-0.09840.19950.22560.20870.16760.08220.3320.2793-0.06920.01520.00780.02120.1445-0.03720.0674-7.992-7.363.281
625.248822.873310.363427.168817.160513.6225-1.21040.32851.9111-1.58810.58721.30860.00370.30220.62330.0823-0.0086-0.24250.06020.14440.1909-25.362-22.25144.311
71.15050.4306-0.09560.18740.0620.3719-0.0088-0.1105-0.0021-0.0421-0.0012-0.05920.0609-0.03150.010.01360.02250.00150.12520.00420.0766-10.0094.43912.14
80.54840.0466-0.18840.3718-0.20620.163-0.0319-0.1658-0.03770.0174-0.0020.02620.078-0.04560.03390.02450.00070.00890.2052-0.01020.0359-18.972-3.17317.981
97.64745.3308-7.72154.6744-9.092322.1563-1.10450.31140.1352-0.2251-0.36520.29121.30181.64521.46970.0351-0.059-0.07030.42430.2678-0.0153-24.4914.853-6.109
101.62750.905-0.20560.62930.20290.8247-0.10240.0241-0.13420.02650.0591-0.03560.04310.18550.0433-0.028-0.0019-0.04110.1067-0.00470.1175-2.1472.08813.089
114.9384-2.1604-4.46632.61782.82024.4880.0166-0.0158-0.1964-0.01830.0670.1365-0.21590.1073-0.0836-0.0040.0308-0.02730.1346-0.00480.0691-8.0719.4016.111
1228.6887-27.6141-21.916726.646921.791323.9499-0.86260.559-1.5971.86980.27091.3808-0.3091-0.17850.59170.1024-0.01170.2036-0.00510.15060.2036-26.28525.25725.126
132.096-0.20821.02290.13-0.27850.7854-0.049-0.0985-0.01970.09640.0141-0.025-0.0135-0.00340.03490.0295-0.00990.04840.1369-0.02140.0141-50.6515.94652.866
140.779-0.26510.57210.2935-0.20480.42060.12980.0459-0.0824-0.0685-0.04220.00670.0340.1126-0.08760.02530.01580.00210.18570.01120.0776-40.762-1.56848.904
1518.1841-0.9302-5.08495.56031.72121.80910.2285-1.6883-0.16170.7237-0.07880.22940.07421.4571-0.14970.12850.01250.00180.25660.0332-0.0861-38.7212.81371.204
160.9757-0.06650.01760.84180.44290.23590.15820.0988-0.11060.0577-0.14870.0404-0.1099-0.0251-0.00950.040.01020.01910.12530.00280.081-55.898-0.1347.614
171.31010.40641.11070.90490.66781.0758-0.0858-0.28910.20670.1272-0.08160.1392-0.1501-0.35780.1674-0.00710.02430.05170.2053-0.00030.0798-58.8519.7353.062
1855.988413.7727-4.13563.3897-0.93594.1339-0.00262.0997-1.2043-0.77880.333-0.2416-0.4335-0.0174-0.33040.11630.01420.25110.0055-0.0230.2148-32.93725.38743.708
192.280.3463-1.01850.0551-0.19661.1673-0.0410.164-0.0156-0.12420.0013-0.04510.0234-0.10590.03970.01750.0133-0.03430.1385-0.00170.0094-50.667-3.82316.493
200.72740.3013-0.85390.1641-0.32391.02510.1482-0.04050.04620.0226-0.04920.0563-0.05540.1767-0.0990.0252-0.01390.01050.18330.01240.0635-40.5613.60120.16
211.22110.53690.37810.23610.16620.1171-0.12550.23910.00710.0969-0.0947-0.0690.0994-0.17660.22020.02520.0412-0.01860.19190.02610.0379-49.334-1.19113.535
221.83990.0989-1.73710.6453-0.29911.70620.10220.17840.07770.2002-0.13770.22530.0462-0.37160.0355-0.03710.0005-0.030.1541-0.01160.102-60.628-2.3321.325
234.3747-5.06861.59886.8377-2.88091.68020.06080.3983-0.5028-0.4493-0.07120.26360.5823-0.47330.01050.0193-0.0674-0.01520.2661-0.07010.0682-54.433-8.49811.198
2429.8259-4.359316.59284.7823-6.678113.59450.1076-0.3919-0.13161.5808-0.2609-1.1426-0.2738-0.41060.15320.0775-0.0103-0.21190.01740.0410.2025-33.938-22.94124.868
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 78
2X-RAY DIFFRACTION2A79 - 145
3X-RAY DIFFRACTION3A146 - 178
4X-RAY DIFFRACTION4A179 - 211
5X-RAY DIFFRACTION5A212 - 228
6X-RAY DIFFRACTION6A229 - 239
7X-RAY DIFFRACTION7B7 - 78
8X-RAY DIFFRACTION8B79 - 144
9X-RAY DIFFRACTION9B145 - 153
10X-RAY DIFFRACTION10B160 - 211
11X-RAY DIFFRACTION11B212 - 228
12X-RAY DIFFRACTION12B229 - 239
13X-RAY DIFFRACTION13C7 - 77
14X-RAY DIFFRACTION14C78 - 144
15X-RAY DIFFRACTION15C145 - 152
16X-RAY DIFFRACTION16C162 - 190
17X-RAY DIFFRACTION17C191 - 228
18X-RAY DIFFRACTION18C229 - 239
19X-RAY DIFFRACTION19D7 - 77
20X-RAY DIFFRACTION20D78 - 145
21X-RAY DIFFRACTION21D146 - 175
22X-RAY DIFFRACTION22D176 - 211
23X-RAY DIFFRACTION23D212 - 228
24X-RAY DIFFRACTION24D229 - 238

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