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

Source organism: Homo sapiens
Biochemical function: protein heterodimerization activity
Biological process: protein neddylation
Cellular component: protein-containing complex

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EC 2.3.2.34: E2 NEDD8-conjugating enzyme

Reaction catalysed:
[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
Systematic name:
[E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine:[E2 NEDD8-conjugating enzyme] [NEDD8-protein]-yl transferase
Alternative Name(s):
  • NEDD8-carrier-protein E2
  • NEDD8-conjugating enzyme E2

EC 6.2.1.64: E1 NEDD8-activating enzyme

Reaction catalysed:
ATP + [NEDD8 protein] + [E1 NEDD8-activating enzyme]-L-cysteine = AMP + diphosphate + [E1 NEDD8-activating enzyme]-S-[NEDD8 protein]-yl-L-cysteine
Systematic name:
[NEDD8 protein]:[E1 NEDD8-activating enzyme] ligase (AMP-forming)
Alternative Name(s):
  • NEDD-activating enzyme E1

GO terms

Sequence families

Pfam Protein families (Pfam)
PF00899
Domain description: ThiF family
Occurring in:
  1. NEDD8-activating enzyme E1 regulatory subunit
  2. NEDD8-activating enzyme E1 catalytic subunit
The deposited structure of PDB entry 1tt5 contains 2 copies of Pfam domain PF00899 (ThiF family) in NEDD8-activating enzyme E1 regulatory subunit. Showing 1 copy in chain A.
The deposited structure of PDB entry 1tt5 contains 2 copies of Pfam domain PF00899 (ThiF family) in NEDD8-activating enzyme E1 catalytic subunit. Showing 1 copy in chain B.

PF08825
Domain description: E2 binding domain
Occurring in:
  1. NEDD8-activating enzyme E1 catalytic subunit
The deposited structure of PDB entry 1tt5 contains 2 copies of Pfam domain PF08825 (E2 binding domain) in NEDD8-activating enzyme E1 catalytic subunit. Showing 1 copy in chain B.

InterPro InterPro annotations
IPR014929
Domain description: E2 binding
Occurring in:
  1. NEDD8-activating enzyme E1 catalytic subunit
IPR000594
Domain description: THIF-type NAD/FAD binding fold
Occurring in:
  1. NEDD8-activating enzyme E1 regulatory subunit
  2. NEDD8-activating enzyme E1 catalytic subunit
IPR045886
Domain description: ThiF/MoeB/HesA family
Occurring in:
  1. NEDD8-activating enzyme E1 regulatory subunit
  2. NEDD8-activating enzyme E1 catalytic subunit
IPR035985
Domain description: Ubiquitin-activating enzyme
Occurring in:
  1. NEDD8-activating enzyme E1 regulatory subunit
  2. NEDD8-activating enzyme E1 catalytic subunit
IPR033127
Domain description: Ubiquitin-activating enzyme E1, Cys active site
Occurring in:
  1. NEDD8-activating enzyme E1 catalytic subunit
IPR023318
Domain description: Ubiquitin activating enzyme, alpha domain superfamily
Occurring in:
  1. NEDD8-activating enzyme E1 catalytic subunit
IPR030468
Domain description: NEDD8-activating enzyme E1 catalytic subunit, N-terminal domain
Occurring in:
  1. NEDD8-activating enzyme E1 catalytic subunit
IPR030667
Domain description: NEDD8-activating enzyme E1 regulatory subunit APP-BP1
Occurring in:
  1. NEDD8-activating enzyme E1 regulatory subunit

Structure domains

CATH CATH domains
3.40.50.720
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Rossmann fold
Homology: NAD(P)-binding Rossmann-like Domain
Occurring in:
  1. NEDD8-activating enzyme E1 regulatory subunit
  2. NEDD8-activating enzyme E1 catalytic subunit
The deposited structure of PDB entry 1tt5 contains 2 copies of CATH domain 3.40.50.720 (Rossmann fold) in NEDD8-activating enzyme E1 regulatory subunit. Showing 1 copy in chain A.
The deposited structure of PDB entry 1tt5 contains 2 copies of CATH domain 3.40.50.720 (Rossmann fold) in NEDD8-activating enzyme E1 catalytic subunit. Showing 1 copy in chain B.
3.10.20.260
Class: Alpha Beta
Architecture: Roll
Topology: Ubiquitin-like (UB roll)
Homology: NEDD8-activating enzyme E1, catalytic subunit
Occurring in:
  1. NEDD8-activating enzyme E1 catalytic subunit
The deposited structure of PDB entry 1tt5 contains 2 copies of CATH domain 3.10.20.260 (Ubiquitin-like (UB roll)) in NEDD8-activating enzyme E1 catalytic subunit. Showing 1 copy in chain B.
1.10.10.520
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Arc Repressor Mutant, subunit A
Homology: Ubiquitin activating enzymes (Uba3). Chain: B, domain 2
Occurring in:
  1. NEDD8-activating enzyme E1 catalytic subunit
The deposited structure of PDB entry 1tt5 contains 2 copies of CATH domain 1.10.10.520 (Arc Repressor Mutant, subunit A) in NEDD8-activating enzyme E1 catalytic subunit. Showing 1 copy in chain B.
SCOP SCOP annotation
89763
Class: Alpha and beta proteins (a/b)
Fold: Activating enzymes of the ubiquitin-like proteins
Superfamily: Activating enzymes of the ubiquitin-like proteins
Occurring in:
  1. NEDD8-activating enzyme E1 regulatory subunit
  2. NEDD8-activating enzyme E1 catalytic subunit
The deposited structure of PDB entry 1tt5 contains 2 copies of SCOP domain 89763 (Ubiquitin activating enzymes (UBA)) in NEDD8-activating enzyme E1 regulatory subunit. Showing 1 copy in chain A.
The deposited structure of PDB entry 1tt5 contains 2 copies of SCOP domain 89763 (Ubiquitin activating enzymes (UBA)) in NEDD8-activating enzyme E1 catalytic subunit. Showing 1 copy in chain B.

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