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- PDB-1tgz: Structure of human Senp2 in complex with SUMO-1 -

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Basic information

Entry
Database: PDB / ID: 1tgz
TitleStructure of human Senp2 in complex with SUMO-1
Components
  • Sentrin-specific protease 2
  • Ubiquitin-like protein SMT3C
KeywordsCELL CYCLE / HYDROLASE / SUMO / AXAM / SENP / ULP / PROTEASE
Function / homology
Function and homology information


SUMO-specific endopeptidase activity / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / deSUMOylase activity / SUMOylation of nuclear envelope proteins / protein desumoylation / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) ...SUMO-specific endopeptidase activity / protein localization to nuclear pore / negative regulation of transcription by transcription factor localization / deSUMOylase activity / SUMOylation of nuclear envelope proteins / protein desumoylation / SUMO is proteolytically processed / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / negative regulation of potassium ion transmembrane transporter activity / PML body organization / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / nuclear stress granule / small protein activating enzyme binding / negative regulation of action potential / SUMOylation of DNA methylation proteins / SUMOylation of immune response proteins / regulation of calcium ion transmembrane transport / XY body / SUMOylation of SUMOylation proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of Wnt signaling pathway / regulation of cardiac muscle cell contraction / Postmitotic nuclear pore complex (NPC) reformation / negative regulation of DNA binding / Maturation of nucleoprotein / negative regulation of protein import into nucleus / SUMOylation of ubiquitinylation proteins / cellular response to cadmium ion / ubiquitin-specific protease binding / transcription factor binding / fat cell differentiation / roof of mouth development / ubiquitin-like protein ligase binding / SUMOylation of transcription factors / protein sumoylation / SUMOylation of DNA replication proteins / postsynaptic cytosol / mRNA transport / potassium channel regulator activity / Regulation of IFNG signaling / nuclear pore / presynaptic cytosol / SUMOylation of DNA damage response and repair proteins / negative regulation of protein ubiquitination / Transcriptional and post-translational regulation of MITF-M expression and activity / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / positive regulation of protein ubiquitination / negative regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / positive regulation of protein-containing complex assembly / protein destabilization / PKR-mediated signaling / PML body / Wnt signaling pathway / Formation of Incision Complex in GG-NER / protein tag activity / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of protein localization / cellular response to heat / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein stabilization / nuclear speck / nuclear body / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / glutamatergic synapse / enzyme binding / proteolysis / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Papain-like cysteine peptidase superfamily ...Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Small ubiquitin-related modifier 1, Ubl domain / Rad60/SUMO-like domain / Ubiquitin-2 like Rad60 SUMO-like / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Small ubiquitin-related modifier 1 / Sentrin-specific protease 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsReverter, D. / Lima, C.D.
CitationJournal: Structure / Year: 2004
Title: A basis for SUMO protease specificity provided by analysis of human Senp2 and a Senp2-SUMO complex
Authors: Reverter, D. / Lima, C.D.
History
DepositionMay 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref / struct_site
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.pdbx_seq_one_letter_code / _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: Sentrin-specific protease 2
B: Ubiquitin-like protein SMT3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5537
Polymers36,0732
Non-polymers4805
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-56 kcal/mol
Surface area14750 Å2
MethodPISA
2
A: Sentrin-specific protease 2
B: Ubiquitin-like protein SMT3C
hetero molecules

A: Sentrin-specific protease 2
B: Ubiquitin-like protein SMT3C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,10614
Polymers72,1454
Non-polymers96110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+1/31
Buried area5340 Å2
ΔGint-127 kcal/mol
Surface area29230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.163, 111.163, 143.106
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Cell settinghexagonal
Space group name H-MP6522

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Components

#1: Protein Sentrin-specific protease 2 / E.C.3.4.22.- / Sentrin/SUMO-specific protease SENP2 / SMT3-specific isopeptidase 2 / Smt3ip2 / Axam2


Mass: 26787.084 Da / Num. of mol.: 1 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Details: CHEMICALLY MODIFIED TO PROMOTE BOND BETWEEN CYS548 AND SUMO-1 GLY97
Source: (gene. exp.) Homo sapiens (human) / Gene: SENP2, KIAA1331 / Plasmid: T7 BASED / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CP RIL
References: UniProt: Q9HC62, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Protein Ubiquitin-like protein SMT3C / Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein UBL1 / Ubiquitin-related protein ...Ubiquitin-homology domain protein PIC1 / Ubiquitin-like protein UBL1 / Ubiquitin-related protein SUMO-1 / GAP modifying protein 1 / GMP1 / Sentrin


Mass: 9285.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBL1, SMT3H3, SMT3C / Plasmid: T7 BASED / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CP RIL / References: UniProt: P63165
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
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: 3.5 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 15, 2004
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 16622 / Num. obs: 15675 / % possible obs: 94.3 % / Observed criterion σ(I): -2 / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 10.8
Reflection shellResolution: 2.8→2.93 Å / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 0.9 / % possible all: 84.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1814230.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 612 5 %RANDOM
Rwork0.226 ---
obs0.2261 12149 90.8 %-
all-13430 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.7793 Å2 / ksol: 0.34907 e/Å3
Displacement parametersBiso mean: 54.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å28.16 Å20 Å2
2--0.1 Å20 Å2
3----0.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 25 81 2608
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.434 81 5.1 %
Rwork0.391 1495 -
obs--72.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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