PDBe 4ddg

X-ray diffraction
3.3Å resolution

Crystal structure of human OTUB1/UbcH5b~Ub/Ub

Released:

Function and Biology Details

Reactions catalysed:
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
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
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).
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin thioesterase OTUB1; Ubiquitin-conjugating enzyme E2 D2 Chains: A, B, C, J, K, L
Molecule details ›
Chains: A, B, C, J, K, L
Length: 399 amino acids
Theoretical weight: 45.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
  • Canonical: Q96FW1 (Residues: 25-271; Coverage: 91%)
  • nullnull
Gene names: HSPC263, OTB1, OTU1, OTUB1, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains:
Structure domains:
Ubiquitin Chains: D, E, F, G, H, I, M, N, O, P, Q, R
Molecule details ›
Chains: D, E, F, G, H, I, M, N, O, P, Q, R
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
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: CLSI BEAMLINE 08ID-1
Spacegroup: P21
Unit cell:
a: 134.566Å b: 104.928Å c: 148.479Å
α: 90° β: 104.19° γ: 90°
R-values:
R R work R free
0.236 0.233 0.28
Expression system: Escherichia coli