› 4ddg

X-ray diffraction
3.3Å resolution

Crystal structure of human OTUB1/UbcH5b~Ub/Ub

Released:
DOI: 10.2210/pdb4ddg/pdb
PDB entry 4ddg coloured by chain, front view.
PDB entry 4ddg coloured by chain, side view.
PDB entry 4ddg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
OTUB1 co-opts Lys48-linked ubiquitin recognition to suppress E2 enzyme function.
Juang YC, Landry MC, Sanches M, Vittal V, Leung CC, Ceccarelli DF, Mateo AR, Pruneda JN, Mao DY, Szilard RK, Orlicky S, Munro M, Brzovic PS, Klevit RE, Sicheri F, Durocher D
Mol Cell 45 384-97 (2012)
PMID: 22325355

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143451 (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%)
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

Quick links

Citations

47 review citations

Mechanisms of Deubiquitinase Specificity and Regulation.
Mevissen et al. (2017)
46 more

14 mentions without citation

Emerging drug development technologies targeting ubiquitination for cancer therapeutics.
Veggiani et al. (2019)
13 more