6o83

X-ray diffraction
3.15Å resolution

S. pombe ubiquitin E1~ubiquitin-AMP tetrahedral intermediate mimic

Released:
Primary publication:
Structural basis for adenylation and thioester bond formation in the ubiquitin E1.
Proc Natl Acad Sci U S A 116 15475-15484 (2019)
PMID: 31235585

Function and Biology Details

Reaction catalysed:
ATP + ubiquitin + [E1 ubiquitin-activating enzyme]-L-cysteine = AMP + diphosphate + S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-131719 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Ubiquitin-activating enzyme E1 1 Chains: A, C
Molecule details ›
Chains: A, C
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:
Ubiquitin Chains: B, D
Molecule details ›
Chains: B, D
Length: 75 amino acids
Theoretical weight: 8.51 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CH07 (Residues: 1-75; Coverage: 59%)
Gene names: SPAC1805.12c, ubi2, uep1
Sequence domains: Ubiquitin family

Ligands and Environments

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 122.575Å b: 150.522Å c: 172.776Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.205 0.203 0.252
Expression system: Escherichia coli