› 4ii2

X-ray diffraction
2.2Å resolution

Crystal structure of Ubiquitin activating enzyme 1 (Uba1) in complex with the Ub E2 Ubc4, ubiquitin, and ATP/Mg

Released:
DOI: 10.2210/pdb4ii2/pdb
PDB entry 4ii2 coloured by chain, front view.
PDB entry 4ii2 coloured by chain, side view.
PDB entry 4ii2 coloured by chain, top view.
Source organism: Schizosaccharomyces pombe 972h-
Primary publication:
Structure of a ubiquitin E1-E2 complex: insights to E1-E2 thioester transfer.
Olsen SK, Lima CD
Mol Cell 49 884-96 (2013)
PMID: 23416107

Function and Biology Details

Reactions catalysed: 
ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine = AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine
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:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-131720 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-activating enzyme E1 1 Chain: A
Molecule details ›
Chain: A
Length: 1001 amino acids
Theoretical weight: 111.76 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: O94609 (Residues: 13-1012; Coverage: 99%)
Gene names: SPBC1604.21c, SPBC211.09, ptr3
Sequence domains:
Structure domains:
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 83 amino acids
Theoretical weight: 9.69 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CH07 (Residues: 1-76; Coverage: 59%)
Gene names: SPAC1805.12c, ubi2, uep1
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Ubiquitin-conjugating enzyme E2 4 Chain: C
Molecule details ›
Chain: C
Length: 163 amino acids
Theoretical weight: 18.19 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: P46595 (Residues: 1-147; Coverage: 100%)
Gene names: SPBC119.02, ubc4
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme

Ligands and Environments

5 bound ligands:
Ligand MG 2 x MG
Ligand ATP 1 x ATP
Ligand PG0 1 x PG0
Ligand EDO 7 x EDO
Ligand SO4 4 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 81.6Å b: 111.2Å c: 181.3Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.214 0.214 0.254
Expression system: Escherichia coli

Quick links

Citations

21 review citations

E2 enzymes: more than just middle men.
Stewart et al. (2016)
20 more

21 mentions without citation

RING-type E3 ligases: master manipulators of E2 ubiquitin-conjugating enzymes and ubiquitination.
Metzger et al. (2014)
20 more