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- PDB-1euv: X-RAY STRUCTURE OF THE C-TERMINAL ULP1 PROTEASE DOMAIN IN COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 1euv
TitleX-RAY STRUCTURE OF THE C-TERMINAL ULP1 PROTEASE DOMAIN IN COMPLEX WITH SMT3, THE YEAST ORTHOLOG OF SUMO.
Components
  • UBITQUTIN-LIKE PROTEIN SMT3
  • ULP1 PROTEASE
KeywordsHYDROLASE / SUMO HYDROLASE / UBIQUITIN-LIKE PROTEASE 1 / SMT3 HYDROLASE DESUMOYLATING ENZYME / CYSTEINE PROTEASE / SUMO PROCESSING ENZYME / SMT3 PROCESSING ENZYME / NABH4 / THIOHEMIACETAL / COVALENT PROTEASE ADDUCT
Function / homology
Function and homology information


Ulp1 peptidase / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation ...Ulp1 peptidase / SUMO is conjugated to E1 (UBA2:SAE1) / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / SUMOylation of transcription factors / SUMOylation of transcription cofactors / Postmitotic nuclear pore complex (NPC) reformation / septin ring / SUMOylation of DNA damage response and repair proteins / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / Major pathway of rRNA processing in the nucleolus and cytosol / ubiquitin-like protein ligase binding / protein sumoylation / cysteine-type peptidase activity / condensed nuclear chromosome / G2/M transition of mitotic cell cycle / protein tag activity / nuclear envelope / nucleolus / proteolysis / identical protein binding / nucleus
Similarity search - Function
Actin-binding Protein, T-fimbrin; domain 1 - #20 / Ubiquitin-related / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Actin-binding Protein, T-fimbrin; domain 1 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / TATA-Binding Protein / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...Actin-binding Protein, T-fimbrin; domain 1 - #20 / Ubiquitin-related / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Actin-binding Protein, T-fimbrin; domain 1 / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / TATA-Binding Protein / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily / Ubiquitin-like (UB roll) / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like-specific protease 1 / Ubiquitin-like protein SMT3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å
AuthorsMossessova, E. / Lima, C.D.
Citation
Journal: Mol.Cell / Year: 2000
Title: Ulp1-SUMO crystal structure and genetic analysis reveal conserved interactions and a regulatory element essential for cell growth in yeast.
Authors: Mossessova, E. / Lima, C.D.
#1: Journal: Nature / Year: 1999
Title: A New Protease Required for Cell-cycle Progression in Yeast.
Authors: Li, S.J. / Hochstrasser, M.
History
DepositionApr 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ULP1 PROTEASE
B: UBITQUTIN-LIKE PROTEIN SMT3


Theoretical massNumber of molelcules
Total (without water)35,6122
Polymers35,6122
Non-polymers00
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint3 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.774, 53.167, 54.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is a monomer constructed from chain A. / The biological assembly is a monomer constructed from chain B.

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Components

#1: Protein ULP1 PROTEASE


Mass: 25650.301 Da / Num. of mol.: 1 / Fragment: C-TERMINAL PROTEASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: Q02724
#2: Protein UBITQUTIN-LIKE PROTEIN SMT3


Mass: 9961.278 Da / Num. of mol.: 1 / Fragment: SMT3 RESIDUES 13-98
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PET28B / Production host: Escherichia coli (E. coli) / References: UniProt: Q12306
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCovalent adduct formed between the proteolytic active site thiol and the C-terminal glycine of Smt3 ...Covalent adduct formed between the proteolytic active site thiol and the C-terminal glycine of Smt3 using the reducing agent NaBH4.
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH6.5, 10% w/v polyethylene glycol 20000, 3% w/v 1,6-hexandiol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 221 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MMES1reservoir
210 %(w/v)PEG200001reservoir
33 %(w/v)1,6-hexandiol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.6→25 Å / Num. all: 49560 / Num. obs: 47875 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 20.694 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 16.4
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.29 / Num. unique all: 4227 / % possible all: 86
Reflection
*PLUS
Num. measured all: 449291
Reflection shell
*PLUS
% possible obs: 86 % / Mean I/σ(I) obs: 3.4

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Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.6→25 Å / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Used a -loglikelihood residual derived from Rice distribution for centric and acentric cases of Fs sparse matrix procedure with anisotropic B-factor refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2378 -5% of the observed data
Rwork0.19 ---
all0.193 49234 --
obs0.193 47560 96.6 %-
Refinement stepCycle: LAST / Resolution: 1.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 0 432 2849
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d1.6

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