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STRUCTURE OF DDB1-DDB2-CUL4A-RBX1 BOUND TO A 12 BP ABASIC SITE CONTAINING DNA-DUPLEX

Source organisms:
Biochemical function: protein binding
Biological process: DNA repair
Cellular component: nucleus

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EC 2.3.2.32: Cullin-RING-type E3 NEDD8 transferase

Reaction catalysed:
S-[NEDD8-protein]-yl-[E2 NEDD8-conjugating enzyme]-L-cysteine + [cullin]-L-lysine = [E2 NEDD8-conjugating enzyme]-L-cysteine + N(6)-[NEDD8-protein]-yl-[cullin]-L-lysine
Systematic name:
S-[NEDD8-protein]-yl-[E2 NEDD8-conjugating enzyme]-L-cysteine:[cullin] [NEDD8-protein] transferase (isopeptide bond-forming; RING-type)
Alternative Name(s):
  • RBX1 (gene name)

EC 2.3.2.27: RING-type E3 ubiquitin transferase

Reaction catalysed:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Systematic name:
[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine:[acceptor protein]-L-lysine ubiquitin transferase (isopeptide bond-forming; RING-type)
Alternative Name(s):
  • RING E3 ligase
  • Ubiquitin transferase RING E3

GO terms

Biochemical function:
Biological process:
Cellular component:

Sequence families

Pfam Protein families (Pfam)
PF00400
Domain description: WD domain, G-beta repeat
Occurring in:
  1. DNA damage-binding protein 2
The deposited structure of PDB entry 4a0k contains 2 copies of Pfam domain PF00400 (WD domain, G-beta repeat) in DNA damage-binding protein 2. Showing 2 copies in chain D.

PF03178
Domain description: CPSF A subunit region
Occurring in:
  1. DNA damage-binding protein 1
The deposited structure of PDB entry 4a0k contains 1 copy of Pfam domain PF03178 (CPSF A subunit region) in DNA damage-binding protein 1. Showing 1 copy in chain C.

PF10433
Domain description: Mono-functional DNA-alkylating methyl methanesulfonate N-term
Occurring in:
  1. DNA damage-binding protein 1
The deposited structure of PDB entry 4a0k contains 1 copy of Pfam domain PF10433 (Mono-functional DNA-alkylating methyl methanesulfonate N-term) in DNA damage-binding protein 1. Showing 1 copy in chain C.

PF12678
Domain description: RING-H2 zinc finger domain
Occurring in:
  1. E3 ubiquitin-protein ligase RBX1, N-terminally processed
The deposited structure of PDB entry 4a0k contains 1 copy of Pfam domain PF12678 (RING-H2 zinc finger domain) in E3 ubiquitin-protein ligase RBX1, N-terminally processed. Showing 1 copy in chain B (this domain is out of the observed residue ranges!).

PF10557
Domain description: Cullin protein neddylation domain
Occurring in:
  1. Cullin-4A
The deposited structure of PDB entry 4a0k contains 1 copy of Pfam domain PF10557 (Cullin protein neddylation domain) in Cullin-4A. Showing 1 copy in chain A.

PF00888
Domain description: Cullin family
Occurring in:
  1. Cullin-4A
The deposited structure of PDB entry 4a0k contains 1 copy of Pfam domain PF00888 (Cullin family) in Cullin-4A. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR001680
Domain description: WD40 repeat
Occurring in:
  1. DNA damage-binding protein 2
IPR015943
Domain description: WD40/YVTN repeat-like-containing domain superfamily
Occurring in:
  1. DNA damage-binding protein 1
  2. DNA damage-binding protein 2
IPR036322
Domain description: WD40-repeat-containing domain superfamily
Occurring in:
  1. DNA damage-binding protein 1
  2. DNA damage-binding protein 2
IPR019559
Domain description: Cullin protein, neddylation domain
Occurring in:
  1. Cullin-4A
IPR016158
Domain description: Cullin homology domain
Occurring in:
  1. Cullin-4A
IPR019775
Domain description: WD40 repeat, conserved site
Occurring in:
  1. DNA damage-binding protein 2
IPR033312
Domain description: DNA damage-binding protein 2
Occurring in:
  1. DNA damage-binding protein 2
IPR004871
Domain description: Cleavage/polyadenylation specificity factor, A subunit, C-terminal
Occurring in:
  1. DNA damage-binding protein 1
IPR018846
Domain description: Cleavage/polyadenylation specificity factor, A subunit, N-terminal
Occurring in:
  1. DNA damage-binding protein 1
IPR001841
Domain description: Zinc finger, RING-type
Occurring in:
  1. E3 ubiquitin-protein ligase RBX1, N-terminally processed
IPR024766
Domain description: Zinc finger, RING-H2-type
Occurring in:
  1. E3 ubiquitin-protein ligase RBX1, N-terminally processed
IPR013083
Domain description: Zinc finger, RING/FYVE/PHD-type
Occurring in:
  1. E3 ubiquitin-protein ligase RBX1, N-terminally processed
IPR016157
Domain description: Cullin, conserved site
Occurring in:
  1. Cullin-4A
IPR036388
Domain description: Winged helix-like DNA-binding domain superfamily
Occurring in:
  1. Cullin-4A
IPR036390
Domain description: Winged helix DNA-binding domain superfamily
Occurring in:
  1. Cullin-4A
IPR036317
Domain description: Cullin homology domain superfamily
Occurring in:
  1. Cullin-4A
IPR001373
Domain description: Cullin, N-terminal
Occurring in:
  1. Cullin-4A
IPR045093
Domain description: Cullin
Occurring in:
  1. Cullin-4A
IPR016159
Domain description: Cullin repeat-like-containing domain superfamily
Occurring in:
  1. Cullin-4A

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