3von

X-ray diffraction
3.15Å resolution

Crystalstructure of the ubiquitin protease

Released:
Source organism: Homo sapiens
Entry authors: Sato Y, Fukai S

Function and Biology Details

Reactions catalysed:
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
Cellular component:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero dimer
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin thioesterase OTUB1 Chains: A, H, O, V, c, j
Molecule details ›
Chains: A, H, O, V, c, j
Length: 228 amino acids
Theoretical weight: 26.53 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96FW1 (Residues: 45-271; Coverage: 84%)
Gene names: HSPC263, OTB1, OTU1, OTUB1
Structure domains:
Ubiquitin-conjugating enzyme E2 variant 2 Chains: B, D, F, I, K, M, P, R, T, W, Y, a, d, f, h, k, m, o
Molecule details ›
Chains: B, D, F, I, K, M, P, R, T, W, Y, a, d, f, h, k, m, o
Length: 138 amino acids
Theoretical weight: 15.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15819 (Residues: 6-143; Coverage: 95%)
Gene names: MMS2, UBE2V2, UEV2
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin-conjugating enzyme E2 N Chains: C, E, G, J, L, N, Q, S, U, X, Z, b, e, g, i, l, n, p
Molecule details ›
Chains: C, E, G, J, L, N, Q, S, U, X, Z, b, e, g, i, l, n, p
Length: 148 amino acids
Theoretical weight: 16.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61088 (Residues: 3-150; Coverage: 97%)
Gene names: BLU, UBE2N
Structure domains: Ubiquitin Conjugating Enzyme

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 102.064Å b: 137.285Å c: 257.109Å
α: 90° β: 90.03° γ: 90°
R-values:
R R work R free
0.226 0.223 0.281
Expression system: Escherichia coli