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

X-ray diffraction
2.6Å resolution
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
Assembly composition:
hetero trimer (preferred)
Entry contents: 3 distinct polypeptide molecules

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Assemblies

Assembly 1
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Assembly Name: NEDD8 E1 activating enzyme complex, NAE1-UBA3 and NEDD8-conjugating enzyme Ubc12
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Multimeric state: hetero trimer
Accessible surface area: 39616.02 Å2
Buried surface area: 8727.46 Å2
Dissociation area: 778.58 Å2
Dissociation energy (ΔGdiss): 5.78 kcal/mol
Dissociation entropy (TΔSdiss): 8.4 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-158198
Assembly 2 (preferred)
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Assembly Name: NEDD8 E1 activating enzyme complex, NAE1-UBA3 and NEDD8-conjugating enzyme Ubc12
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Multimeric state: hetero trimer
Accessible surface area: 38632.52 Å2
Buried surface area: 7795.15 Å2
Dissociation area: 610.68 Å2
Dissociation energy (ΔGdiss): 1.96 kcal/mol
Dissociation entropy (TΔSdiss): 7.64 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-158198

Macromolecules

NEDD8-activating enzyme E1 regulatory subunit
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%)
  • Best match: Q13564-4 (Residues: 1-537)
Gene names: APPBP1, HPP1, NAE1
Pfam: ThiF family
InterPro:
CATH: NAD(P)-binding Rossmann-like Domain
SCOP: Ubiquitin activating enzymes (UBA)
NEDD8-activating enzyme E1 regulatory subunit in PDB entry 1tt5, assembly 2, front view.
NEDD8-activating enzyme E1 regulatory subunit in PDB entry 1tt5, assembly 2, side view.
NEDD8-activating enzyme E1 regulatory subunit in PDB entry 1tt5, assembly 2, top view.
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NEDD8-activating enzyme E1 catalytic subunit
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
Pfam:
InterPro:
CATH:
SCOP: Ubiquitin activating enzymes (UBA)
NEDD8-activating enzyme E1 catalytic subunit in PDB entry 1tt5, assembly 2, front view.
NEDD8-activating enzyme E1 catalytic subunit in PDB entry 1tt5, assembly 2, side view.
NEDD8-activating enzyme E1 catalytic subunit in PDB entry 1tt5, assembly 2, top view.
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NEDD8-conjugating enzyme Ubc12
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
NEDD8-conjugating enzyme Ubc12 in PDB entry 1tt5, assembly 2, front view.
NEDD8-conjugating enzyme Ubc12 in PDB entry 1tt5, assembly 2, side view.
NEDD8-conjugating enzyme Ubc12 in PDB entry 1tt5, assembly 2, top view.
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