› 1tt5

X-ray diffraction
2.6Å resolution

Structure of APPBP1-UBA3-Ubc12N26: a unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8

Released:
DOI: 10.2210/pdb1tt5/pdb
PDB entry 1tt5 coloured by chain, front view.
PDB entry 1tt5 coloured by chain, side view.
PDB entry 1tt5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8.
Huang DT, Miller DW, Mathew R, Cassell R, Holton JM, Roussel MF, Schulman BA
Nat Struct Mol Biol 11 927-35 (2004)
PMID: 15361859

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 domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158198 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
NEDD8-activating enzyme E1 regulatory subunit Chains: A, C
Molecule details ›
Chains: A, C
Length: 531 amino acids
Theoretical weight: 59.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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
Molecule details ›
Chains: B, D
Length: 434 amino acids
Theoretical weight: 48.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8TBC4 (Residues: 33-463; Coverage: 93%)
Gene names: UBA3, UBE1C
Sequence domains:
Structure domains:
NEDD8-conjugating enzyme Ubc12 Chains: E, F
Molecule details ›
Chains: E, F
Length: 26 amino acids
Theoretical weight: 2.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61081 (Residues: 1-26; Coverage: 14%)
Gene names: UBC12, UBE2M

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 92.41Å b: 122.77Å c: 195.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.237 0.237 0.279
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

28 review citations

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

6 mentions without citation

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