PDBe 5aek

X-ray diffraction
3Å resolution

Crystal structure of the human SENP2 C548S in complex with the human SUMO1 K48M F66W

Released:
Source organism: Homo sapiens
Entry authors: Gallego P, Grana-Montes R, Espargaro A, Castillo V, Torrent J, Lange R, Papaleo E, Lindorff-Larsend K, Ventura S, Reverter D

Function and Biology Details

Reaction catalysed:
Hydrolysis of the alpha-linked peptide bond in the sequence Gly-Gly-|-Ala-Thr-Tyr at the C-terminal end of the small ubiquitin-like modifier (SUMO) propeptide, Smt3, leading to the mature form of the protein. A second reaction involves the cleavage of an epsilon-linked peptide bond between the C-terminal glycine of the mature SUMO and the lysine epsilon-amino group of the target protein.
Biochemical function:
Biological process:
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Sentrin-specific protease 2 Chains: A, C, E, G, I, K, M, O, Q, S, U, W
Molecule details ›
Chains: A, C, E, G, I, K, M, O, Q, S, U, W
Length: 224 amino acids
Theoretical weight: 26.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: NEW Q9HC62 (Residues: 366-589; Coverage: 38%)
Gene names: KIAA1331, SENP2
Sequence domains: Ulp1 protease family, C-terminal catalytic domain
Structure domains: Adenoviral Proteinase; Chain A
Small ubiquitin-related modifier 1 Chains: B, D, F, H, J, L, N, P, R, T, V, X
Molecule details ›
Chains: B, D, F, H, J, L, N, P, R, T, V, X
Length: 78 amino acids
Theoretical weight: 9.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: NEW P63165 (Residues: 20-97; Coverage: 77%)
Gene names: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1
Sequence domains: Ubiquitin-2 like Rad60 SUMO-like
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: P2
Unit cell:
a: 113.721Å b: 119.319Å c: 199.84Å
α: 90° β: 89.67° γ: 90°
R-values:
R R work R free
0.259 0.257 0.326
Expression system: Escherichia coli