› 4ldt

X-ray diffraction
1.9Å resolution

The structure of h/ceOTUB1-ubiquitin aldehyde-UBCH5B~Ub

Released:
DOI: 10.2210/pdb4ldt/pdb
PDB entry 4ldt coloured by chain, front view.
PDB entry 4ldt coloured by chain, side view.
PDB entry 4ldt coloured by chain, top view.
Source organisms:
Primary publication:
E2 ubiquitin-conjugating enzymes regulate the deubiquitinating activity of OTUB1.
Wiener R, DiBello AT, Lombardi PM, Guzzo CM, Zhang X, Matunis MJ, Wolberger C
Nat Struct Mol Biol 20 1033-9 (2013)
PMID: 23955022

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
(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
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-143330 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ubiquitin thioesterase OTUB1; Ubiquitin thioesterase otubain-like Chain: A
Molecule details ›
Chain: A
Length: 288 amino acids
Theoretical weight: 32.8 KDa
Source organisms: Expression system: Escherichia coli
UniProt:
  • Canonical: Q96FW1 (Residues: 1-48; Coverage: 18%)
  • Canonical: Q9XVR6 (Residues: 45-284; Coverage: 85%)
Gene names: C25D7.8, HSPC263, OTB1, OTU1, OTUB1, otub-1
Sequence domains: Peptidase C65 Otubain
Structure domains:
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.56 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
Ubiquitin-conjugating enzyme E2 D2 Chain: C
Molecule details ›
Chain: C
Length: 148 amino acids
Theoretical weight: 16.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin Chain: D
Molecule details ›
Chain: D
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

2 bound ligands:
Ligand EDO 4 x EDO
Ligand MG 1 x MG
1 modified residue:
Ligand GLZ 1 x GLZ

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21212
Unit cell:
a: 104.894Å b: 131.612Å c: 46.501Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.192 0.223
Expression system: Escherichia coli

Quick links

Citations

20 review citations

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

7 mentions without citation

Mechanisms for regulating deubiquitinating enzymes.
Wolberger C. (2014)
6 more