› 3dbr

X-ray diffraction
3.05Å resolution

Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg)

Released:
DOI: 10.2210/pdb3dbr/pdb
PDB entry 3dbr coloured by chain, front view.
PDB entry 3dbr coloured by chain, side view.
PDB entry 3dbr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural dissection of a gating mechanism preventing misactivation of ubiquitin by NEDD8's E1.
Souphron J, Waddell MB, Paydar A, Tokgöz-Gromley Z, Roussel MF, Schulman BA
Biochemistry 47 8961-9 (2008)
PMID: 18652489

Function and Biology Details

Reaction catalysed: 
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine = AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171762 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
NEDD8-activating enzyme E1 regulatory subunit Chains: A, C, E, G
Molecule details ›
Chains: A, C, E, G
Length: 531 amino acids
Theoretical weight: 59.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13564 (Residues: 1-534; Coverage: 99%)
Gene names: APPBP1, HPP1, NAE1
Sequence domains: ThiF family
Structure domains: NAD(P)-binding Rossmann-like Domain
NEDD8-activating enzyme E1 catalytic subunit Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 434 amino acids
Theoretical weight: 48.74 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TBC4 (Residues: 33-463; Coverage: 93%)
Gene names: UBA3, UBE1C
Sequence domains:
Structure domains:
NEDD8 Chains: I, J, K, L
Molecule details ›
Chains: I, J, K, L
Length: 88 amino acids
Theoretical weight: 9.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15843 (Residues: 1-76; Coverage: 94%)
Gene name: NEDD8
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X25
Spacegroup: P212121
Unit cell:
a: 134.322Å b: 198.531Å c: 208.795Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.23 0.23 0.28
Expression system: Escherichia coli

Quick links

Citations

12 review citations

Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways.
Schulman et al. (2009)
11 more

4 mentions without citation

Anticancer drug discovery by targeting cullin neddylation.
Yu et al. (2020)
3 more