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- PDB-4pqt: Insights into the mechanism of deubiquitination by JAMM deubiquit... -

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Basic information

Entry
Database: PDB / ID: 4pqt
TitleInsights into the mechanism of deubiquitination by JAMM deubiquitinases from co-crystal structures of enzyme with substrate and product
Components
  • AMSH-like protease sst2
  • Protein UBBP4
KeywordsHydrolase/transcription / helix-beta-helix sandwich / ubiquitin / deubiquitination / Zinc metalloprotease / Lysine 63-linked polyubiquitin / Hydrolase-transcription complex
Function / homology
Function and homology information


Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / late endosome to vacuole transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding ...Metalloprotease DUBs / cytoplasm to vacuole targeting by the NVT pathway / late endosome to vacuole transport via multivesicular body sorting pathway / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / late endosome to vacuole transport / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / K63-linked deubiquitinase activity / K63-linked polyubiquitin modification-dependent protein binding / cell division site / ubiquitin binding / endosome / zinc ion binding / membrane / cytoplasm
Similarity search - Function
STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. ...STAMBP/STALP-like, MPN domain / USP8 dimerisation domain / USP8 dimerisation domain / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / AMSH-like protease sst2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsShrestha, R.K. / Ronau, J.A. / Das, C.
CitationJournal: Biochemistry / Year: 2014
Title: Insights into the Mechanism of Deubiquitination by JAMM Deubiquitinases from Cocrystal Structures of the Enzyme with the Substrate and Product.
Authors: Shrestha, R.K. / Ronau, J.A. / Davies, C.W. / Guenette, R.G. / Strieter, E.R. / Paul, L.N. / Das, C.
History
DepositionMar 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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: AMSH-like protease sst2
B: Protein UBBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1786
Polymers30,9262
Non-polymers2524
Water1,40578
1
A: AMSH-like protease sst2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1274
Polymers21,9381
Non-polymers1903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein UBBP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0502
Polymers8,9881
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-11 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.413, 58.003, 56.189
Angle α, β, γ (deg.)90.00, 108.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein AMSH-like protease sst2 / Suppressor of ste12 deletion protein 2


Mass: 21937.723 Da / Num. of mol.: 1 / Fragment: Catalytic domain unp residues 245-435 / Mutation: D354A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: SPAC19B12.10, sst2 / Plasmid: pGEX-6-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: Q9P371, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Protein Protein UBBP4


Mass: 8988.284 Da / Num. of mol.: 1 / Fragment: unp residues 77-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBBP4, Ubiquitin / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: J3QRK5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1% w/v Tryptone, 0.05M HEPES sodium, 20% PEG 3,350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 9, 2013
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.05→60 Å / Num. all: 16438 / Num. obs: 16438 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 16.8
Reflection shellResolution: 2.05→2.05 Å / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.625 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 4K1R

4k1r


Resolution: 2.05→40.109 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 832 5.07 %Random
Rwork0.2019 ---
obs0.2045 16420 99.68 %-
all-16585 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→40.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 13 78 2133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082090
X-RAY DIFFRACTIONf_angle_d1.2132824
X-RAY DIFFRACTIONf_dihedral_angle_d14.09782
X-RAY DIFFRACTIONf_chiral_restr0.045333
X-RAY DIFFRACTIONf_plane_restr0.007358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.044-2.17210.32811400.28572547X-RAY DIFFRACTION98
2.1721-2.33980.28551270.25752605X-RAY DIFFRACTION100
2.3398-2.57520.29461350.25062592X-RAY DIFFRACTION100
2.5752-2.94770.33641320.23892607X-RAY DIFFRACTION100
2.9477-3.71340.26911390.19562599X-RAY DIFFRACTION100
3.7134-40.11650.18151590.14762638X-RAY DIFFRACTION100

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