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- PDB-5aek: Crystal structure of the human SENP2 C548S in complex with the hu... -

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Basic information

Entry
Database: PDB / ID: 5aek
TitleCrystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W
Components
  • SENTRIN-SPECIFIC PROTEASE 2
  • SMALL UBIQUITIN-RELATED MODIFIER 1
KeywordsHYDROLASE / SUMO / SENP / FOLDING EVOLUTION
Function / homology
Function and homology information


SUMO-specific endopeptidase activity / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / deSUMOylase activity / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / protein desumoylation / nuclear stress granule ...SUMO-specific endopeptidase activity / negative regulation of transcription by transcription factor localization / SUMOylation of nuclear envelope proteins / deSUMOylase activity / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMO is proteolytically processed / negative regulation of delayed rectifier potassium channel activity / SUMO is conjugated to E1 (UBA2:SAE1) / protein desumoylation / nuclear stress granule / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / negative regulation of action potential / small protein activating enzyme binding / SUMOylation of DNA methylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of immune response proteins / Maturation of nucleoprotein / SUMOylation of RNA binding proteins / regulation of Wnt signaling pathway / Postmitotic nuclear pore complex (NPC) reformation / Maturation of nucleoprotein / negative regulation of protein import into nucleus / ubiquitin-specific protease binding / SUMOylation of ubiquitinylation proteins / roof of mouth development / fat cell differentiation / negative regulation of DNA binding / ubiquitin-like protein ligase binding / SUMOylation of DNA replication proteins / protein sumoylation / transcription factor binding / SUMOylation of transcription factors / mRNA transport / potassium channel regulator activity / SUMOylation of DNA damage response and repair proteins / nuclear pore / Regulation of IFNG signaling / negative regulation of protein ubiquitination / cellular response to cadmium ion / SUMOylation of chromatin organization proteins / SUMOylation of transcription cofactors / positive regulation of protein ubiquitination / positive regulation of protein-containing complex assembly / protein destabilization / SUMOylation of intracellular receptors / PKR-mediated signaling / negative regulation of DNA-binding transcription factor activity / PML body / protein tag activity / Wnt signaling pathway / Formation of Incision Complex in GG-NER / regulation of protein localization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / cellular response to heat / nuclear membrane / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein stabilization / nuclear body / nuclear speck / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / nucleolus / enzyme binding / proteolysis / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Adenoviral Proteinase; Chain / Adenoviral Proteinase; Chain A / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / 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 / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / 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-like domain / Ubiquitin domain profile. / 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: 3 Å
AuthorsGallego, P. / Grana-Montes, R. / Espargaro, A. / Castillo, V. / Torrent, J. / Lange, R. / Papaleo, E. / Lindorff-Larsend, K. / Ventura, S. / Reverter, D.
CitationJournal: To be Published
Title: Stepping Back and Forward on Sumo Folding Evolution
Authors: Grana-Montes, R. / Gallego, P. / Espargaro, A. / Castillo, V. / Torrent, J. / Lange, R. / Reverter, D. / Papaleo, E. / Lindorff-Larsend, K. / Ventura, S.
History
DepositionDec 23, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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: SMALL UBIQUITIN-RELATED MODIFIER 1
C: SENTRIN-SPECIFIC PROTEASE 2
D: SMALL UBIQUITIN-RELATED MODIFIER 1
E: SENTRIN-SPECIFIC PROTEASE 2
F: SMALL UBIQUITIN-RELATED MODIFIER 1
G: SENTRIN-SPECIFIC PROTEASE 2
H: SMALL UBIQUITIN-RELATED MODIFIER 1
I: SENTRIN-SPECIFIC PROTEASE 2
J: SMALL UBIQUITIN-RELATED MODIFIER 1
K: SENTRIN-SPECIFIC PROTEASE 2
L: SMALL UBIQUITIN-RELATED MODIFIER 1
M: SENTRIN-SPECIFIC PROTEASE 2
N: SMALL UBIQUITIN-RELATED MODIFIER 1
O: SENTRIN-SPECIFIC PROTEASE 2
P: SMALL UBIQUITIN-RELATED MODIFIER 1
Q: SENTRIN-SPECIFIC PROTEASE 2
R: SMALL UBIQUITIN-RELATED MODIFIER 1
S: SENTRIN-SPECIFIC PROTEASE 2
T: SMALL UBIQUITIN-RELATED MODIFIER 1
U: SENTRIN-SPECIFIC PROTEASE 2
V: SMALL UBIQUITIN-RELATED MODIFIER 1
W: SENTRIN-SPECIFIC PROTEASE 2
X: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)428,19824
Polymers428,19824
Non-polymers00
Water0
1
A: SENTRIN-SPECIFIC PROTEASE 2
B: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-6.4 kcal/mol
Surface area17430 Å2
MethodPQS
2
C: SENTRIN-SPECIFIC PROTEASE 2
D: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-8.9 kcal/mol
Surface area17590 Å2
MethodPQS
3
E: SENTRIN-SPECIFIC PROTEASE 2
F: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-5.7 kcal/mol
Surface area17890 Å2
MethodPQS
4
G: SENTRIN-SPECIFIC PROTEASE 2
H: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-7.7 kcal/mol
Surface area17570 Å2
MethodPQS
5
I: SENTRIN-SPECIFIC PROTEASE 2
J: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-6.6 kcal/mol
Surface area17380 Å2
MethodPQS
6
K: SENTRIN-SPECIFIC PROTEASE 2
L: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-4.3 kcal/mol
Surface area18060 Å2
MethodPQS
7
M: SENTRIN-SPECIFIC PROTEASE 2
N: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-8.7 kcal/mol
Surface area17620 Å2
MethodPQS
8
O: SENTRIN-SPECIFIC PROTEASE 2
P: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-6.2 kcal/mol
Surface area17440 Å2
MethodPQS
9
Q: SENTRIN-SPECIFIC PROTEASE 2
R: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-4.3 kcal/mol
Surface area17340 Å2
MethodPQS
10
S: SENTRIN-SPECIFIC PROTEASE 2
T: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-7.7 kcal/mol
Surface area17390 Å2
MethodPQS
11
U: SENTRIN-SPECIFIC PROTEASE 2
V: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-9.4 kcal/mol
Surface area17990 Å2
MethodPQS
12
W: SENTRIN-SPECIFIC PROTEASE 2
X: SMALL UBIQUITIN-RELATED MODIFIER 1


Theoretical massNumber of molelcules
Total (without water)35,6832
Polymers35,6832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-7.8 kcal/mol
Surface area17960 Å2
MethodPQS
Unit cell
Length a, b, c (Å)113.721, 119.319, 199.840
Angle α, β, γ (deg.)90.00, 89.67, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
SENTRIN-SPECIFIC PROTEASE 2 / AXAM2 / SMT3-SPECIFIC ISOPEPTIDASE 2 / SMT3IP2 / SENTRIN/SUMO-SPECIFIC PROTEASE SENP2


Mass: 26542.773 Da / Num. of mol.: 12 / Fragment: CATALYTIC DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9HC62, Ulp1 peptidase
#2: Protein
SMALL UBIQUITIN-RELATED MODIFIER 1 / SUMO-1 / GAP-MODIFYING PROTEIN 1 / GMP1 / SMT3 HOMOLOG 3 / SENT RIN / UBIQUITIN-HOMOLOGY DOMAIN ...SUMO-1 / GAP-MODIFYING PROTEIN 1 / GMP1 / SMT3 HOMOLOG 3 / SENT RIN / UBIQUITIN-HOMOLOGY DOMAIN PROTEIN PIC1 / UBIQUITIN-LIKE PROTEI N SMT3C / SMT3C / UBIQUITIN-LIKE PROTEIN UBL1


Mass: 9140.415 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P63165

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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: 3.14 Å3/Da / Density % sol: 60.79 % / Description: NONE
Crystal growTemperature: 291 K
Details: 2M AMMONIUM SULFATE, 5% PEG 400, 0.1M BIS-TRIS PH 6.5 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979491
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979491 Å / Relative weight: 1
ReflectionResolution: 3→46.76 Å / Num. obs: 101157 / % possible obs: 94.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 3.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.4 / % possible all: 87.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XPSdata reduction
CCP4Idata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TGZ

1tgz


Resolution: 3→47 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.835 / SU B: 24.349 / SU ML: 0.457 / Cross valid method: THROUGHOUT / ESU R Free: 0.552 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.32625 3167 3.1 %RANDOM
Rwork0.25688 ---
obs0.25935 97738 97.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.789 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20.33 Å2
2--1.56 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 3→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29972 0 0 0 29972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02230658
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5961.95341263
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.21253588
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.39124.5091508
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.02155957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.09115156
X-RAY DIFFRACTIONr_chiral_restr0.1080.24393
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02122856
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5691.517977
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.094229135
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.325312681
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7724.512128
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.453 67 -
Rwork0.329 6330 -
obs--91.92 %

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