› 2nvu

X-ray diffraction
2.8Å resolution

Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex

Released:
DOI: 10.2210/pdb2nvu/pdb
PDB entry 2nvu coloured by chain, front view.
PDB entry 2nvu coloured by chain, side view.
PDB entry 2nvu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity.
Huang DT, Hunt HW, Zhuang M, Ohi MD, Holton JM, Schulman BA
Nature 445 394-8 (2007)
PMID: 17220875

Function and Biology Details

Reactions catalysed: 
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine = AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
[E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine + [E2 NEDD8-conjugating enzyme]-L-cysteine = [E1 NEDD8-activating enzyme]-L-cysteine + [E2 NEDD8-conjugating enzyme]-S-[NEDD8-protein]-yl-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158197 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
NEDD8-activating enzyme E1 regulatory subunit Chain: A
Molecule details ›
Chain: A
Length: 536 amino acids
Theoretical weight: 60.46 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13564 (Residues: 1-534; Coverage: 100%)
Gene names: APPBP1, HPP1, NAE1
Sequence domains: ThiF family
Structure domains: NAD(P)-binding Rossmann-like Domain
NEDD8-activating enzyme E1 catalytic subunit Chain: B
Molecule details ›
Chain: B
Length: 805 amino acids
Theoretical weight: 89.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8TBC4 (Residues: 31-463; Coverage: 94%)
Gene names: UBA3, UBE1C
Sequence domains:
Structure domains:
NEDD8-conjugating enzyme Ubc12 Chain: C
Molecule details ›
Chain: C
Length: 180 amino acids
Theoretical weight: 20.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61081 (Residues: 1-183; Coverage: 97%)
Gene names: UBC12, UBE2M
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Ubiquitin-like protein NEDD8 Chains: I, J
Molecule details ›
Chains: I, J
Length: 81 amino acids
Theoretical weight: 8.92 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

3 bound ligands:
Ligand MG 1 x MG
Ligand ZN 1 x ZN
Ligand ATP 1 x ATP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P3221
Unit cell:
a: 156.494Å b: 156.494Å c: 190.485Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.241 0.241 0.274
Expression system: Escherichia coli

Quick links

Citations

34 review citations

Building ubiquitin chains: E2 enzymes at work.
Ye et al. (2009)
33 more

28 mentions without citation

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