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- PDB-2ylm: Mechanism of USP7 (HAUSP) activation by its C-terminal ubiquitin-... -

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Basic information

Entry
Database: PDB / ID: 2ylm
TitleMechanism of USP7 (HAUSP) activation by its C-terminal ubiquitin-like domain (HUBL) and allosteric regulation by GMP-synthetase.
ComponentsUBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7
KeywordsHYDROLASE / UBL
Function / homology
Function and homology information


regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity ...regulation of telomere capping / monoubiquitinated protein deubiquitination / regulation of retrograde transport, endosome to Golgi / deubiquitinase activity / DNA alkylation repair / regulation of DNA-binding transcription factor activity / K48-linked deubiquitinase activity / symbiont-mediated disruption of host cell PML body / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of NF-kappaB transcription factor activity / protein deubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / transcription-coupled nucleotide-excision repair / negative regulation of gluconeogenesis / negative regulation of TORC1 signaling / Regulation of PTEN localization / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of signal transduction by p53 class mediator / regulation of protein stability / regulation of circadian rhythm / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / PML body / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / rhythmic process / Regulation of TP53 Degradation / p53 binding / chromosome / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / nuclear body / protein stabilization / Ub-specific processing proteases / protein ubiquitination / cysteine-type endopeptidase activity / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytosol
Similarity search - Function
Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Ubiquitin specific protease (USP) domain signature 2. ...Ubiquitin carboxyl-terminal hydrolase 7, ICP0-binding domain / ICP0-binding domain of Ubiquitin-specific protease 7 / Ubiquitin carboxyl-terminal hydrolase, C-terminal / Ubiquitin-specific protease C-terminal / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / 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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase 7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsFaesen, A.C. / Perrakis, A. / Sixma, T.K.
CitationJournal: Mol.Cell / Year: 2011
Title: Mechanism of Usp7/Hausp Activation by its C- Terminal Ubiquitin-Like Domain and Allosteric Regulation by Gmp-Synthetase
Authors: Faesen, A.C. / Dirac, A.M.G. / Shanmugham, A. / Ovaa, H. / Perrakis, A. / Sixma, T.K.
History
DepositionJun 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2Jan 15, 2014Group: Atomic model / Other
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9652
Polymers61,9291
Non-polymers351
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.980, 82.310, 150.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7 / UBIQUITIN SPECIFIC PROTEASE 7 / DEUBIQUITINATING ENZYME 7 / HERPESVIRUS-ASSOCIATED UBIQUITIN- ...UBIQUITIN SPECIFIC PROTEASE 7 / DEUBIQUITINATING ENZYME 7 / HERPESVIRUS-ASSOCIATED UBIQUITIN-SPECIFIC PROTEASE / UBIQUITIN THIOESTERASE 7 / UBIQUITIN-SPECIFIC-PROCESSING PROTEASE 7


Mass: 61929.438 Da / Num. of mol.: 1
Fragment: USP7 UBIQUITIN-LIKE DOMAIN (HUBL), RESIDUES 560-1084
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q93009, 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.: 128 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL LINKER AFTER CLEAVAGE.

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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: 3.9 Å3/Da / Density % sol: 68.46 % / Description: NONE
Crystal growpH: 6 / Details: 10% PEG 4000, 200 MM NACL, 100 MM MES PH 6.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 11, 2009 / Details: PT COATED MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.7→39.7 Å / Num. obs: 27939 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 90.56 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
iMOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.7→37.78 Å / Cor.coef. Fo:Fc: 0.9409 / Cor.coef. Fo:Fc free: 0.9279 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 1401 5.01 %RANDOM
Rwork0.191 ---
obs0.1923 27939 --
Displacement parametersBiso mean: 83.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.8004 Å20 Å20 Å2
2---10.7899 Å20 Å2
3---9.9895 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.7→37.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4340 0 1 128 4469
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094440HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.075995HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2104SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes138HARMONIC2
X-RAY DIFFRACTIONt_gen_planes624HARMONIC5
X-RAY DIFFRACTIONt_it4440HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.92
X-RAY DIFFRACTIONt_other_torsion3.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion555SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4693SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.8 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3103 135 4.66 %
Rwork0.2365 2765 -
all0.2399 2900 -
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)
14.67472.05410.61443.18140.35811.1054-0.2160.3511-0.2059-0.41230.24140.08450.06780.0467-0.0253-0.06440.06950.0284-0.14180.012-0.2557-12.920853.102311.5251
27.0236-2.3080.64286.3724-2.86798.1852-0.0457-0.07090.22040.54420.18880.4546-0.5442-0.434-0.1431-0.0450.14070.0502-0.13720.152-0.2801-7.223943.177849.7005
34.6239-0.24352.69112.9-0.86646.5384-0.1177-0.37630.2292-0.20440.0931-0.0574-0.05330.13440.0246-0.3016-0.04050.089-0.1701-0.0941-0.07828.267333.274886.562
40.19830.35590.185200.31880.62480.0087-0.048-0.01820.0465-0.0008-0.00270.0254-0.0258-0.00790.0066-0.0962-0.11670.1571-0.0826-0.156718.872928.2985108.497
50-0.9245-2.457102.37140.11320.0281-0.1107-0.01870.140.01610.08820.0087-0.0751-0.0442-0.0182-0.11880.09390.17850.0476-0.19645.116724.6979108.104
60.054-0.1144-0.12470.6449-0.739800.00740.015-0.01330.00940.00950.01140.00280.0162-0.01690.076-0.0494-0.0048-0.03560.11850.036614.75411.4158100.976
70.1213-0.06070.12770-0.07170.10790.0016-0.01140.0006-0.01010.0015-0.01110.0015-0.0031-0.00310.08630.06550.03790.09390.06870.00715.101619.2071114.616
81.9691-0.51552.2861.1359-1.87441.10760.0028-0.0347-0.10320.1140.0744-0.0610.1539-0.0692-0.0772-0.2445-0.0855-0.08280.0730.00490.00217.289719.732597.2886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 555-792)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 793-884)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 885-1009)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 1010-1017)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 1018-1044)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 1045-1051)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 1052-1057)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 1058-1083)

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