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- PDB-4msq: Crystal structure of Schizosaccharomyces pombe AMSH-like protease... -

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Basic information

Entry
Database: PDB / ID: 4msq
TitleCrystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 catalytic domain bound to ubiquitin
Components
  • AMSH-like protease sst2
  • Ubiquitin
KeywordsHYDROLASE/PROTEIN BINDING / ubiquitin / deubiquitination / Helix-beta-helix sandwich / Zinc metalloprotease / lysine 63-linked polyubiquitin / cytosol / endosome / HYDROLASE-PROTEIN BINDING 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 polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity ...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 polyubiquitin modification-dependent protein binding / K63-linked deubiquitinase activity / cell division site / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Translesion synthesis by POLI / Regulation of activated PAK-2p34 by proteasome mediated degradation / IKK complex recruitment mediated by RIP1 / ubiquitin binding / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / activated TAK1 mediates p38 MAPK activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Vpu mediated degradation of CD4 / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling
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. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Polyubiquitin-C / AMSH-like protease sst2
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.952 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
DepositionSep 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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: Ubiquitin
C: AMSH-like protease sst2
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,10422
Polymers61,9404
Non-polymers1,16318
Water5,495305
1
A: AMSH-like protease sst2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,53511
Polymers30,9702
Non-polymers5659
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-33 kcal/mol
Surface area12140 Å2
MethodPISA
2
C: AMSH-like protease sst2
D: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,56811
Polymers30,9702
Non-polymers5989
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-38 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.244, 57.032, 81.175
Angle α, β, γ (deg.)90.00, 104.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 21981.732 Da / Num. of mol.: 2 / Fragment: catalytic domain, UNP residues 245-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972/ATCC 24843 / Gene: sst2, SPAC19B12.10 / 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 Ubiquitin


Mass: 8988.284 Da / Num. of mol.: 2 / Fragment: UNP residues 77-152
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC, Ubiquitin / Plasmid: pGEX-6-P1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P0CG48

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Non-polymers , 4 types, 323 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.58 Å3/Da / Density % sol: 52.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2 M Sodium citrate tribasic dihydrate, 20% w/v PEG 3350, pH 7.6, 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: Feb 3, 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: 1.97→50 Å / Num. obs: 45372 / % possible obs: 98.7 % / Observed criterion σ(F): 3.4 / Observed criterion σ(I): 3.4 / Redundancy: 7.5 % / Rmerge(I) obs: 0.139 / Rsym value: 0.139 / Net I/σ(I): 21
Reflection shellResolution: 1.97→2 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
AutoSolphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.952→41.279 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.04 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 2288 5.04 %Random
Rwork0.1769 ---
all0.1785 46049 --
obs0.1769 45363 98.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.952→41.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 61 305 4444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074235
X-RAY DIFFRACTIONf_angle_d1.1015714
X-RAY DIFFRACTIONf_dihedral_angle_d13.7931584
X-RAY DIFFRACTIONf_chiral_restr0.072671
X-RAY DIFFRACTIONf_plane_restr0.005721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9524-1.99480.28721350.2212581X-RAY DIFFRACTION96
1.9948-2.04120.28461510.21682614X-RAY DIFFRACTION97
2.0412-2.09230.26171450.19862637X-RAY DIFFRACTION98
2.0923-2.14880.21221350.18752683X-RAY DIFFRACTION98
2.1488-2.21210.24761400.1832636X-RAY DIFFRACTION98
2.2121-2.28350.19791200.17792716X-RAY DIFFRACTION98
2.2835-2.36510.22611370.18632664X-RAY DIFFRACTION99
2.3651-2.45970.2521300.18072732X-RAY DIFFRACTION99
2.4597-2.57170.23431360.18052649X-RAY DIFFRACTION99
2.5717-2.70720.2161400.17782705X-RAY DIFFRACTION99
2.7072-2.87680.21161480.19052712X-RAY DIFFRACTION99
2.8768-3.09890.21531550.18952709X-RAY DIFFRACTION100
3.0989-3.41060.18981540.17952726X-RAY DIFFRACTION99
3.4106-3.90380.21441520.16842727X-RAY DIFFRACTION100
3.9038-4.91710.15871620.14482743X-RAY DIFFRACTION100
4.9171-41.2880.18461480.17582841X-RAY DIFFRACTION100

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