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Cryo-EM structure of RAG in complex with 12-RSS substrate DNA

Source organisms:
Biochemical function: metal ion binding
Biological process: V(D)J recombination
Cellular component: endodeoxyribonuclease complex

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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

Sequence families

Pfam Protein families (Pfam)
PF13341
Domain description: RAG2 PHD domain
Occurring in:
  1. V(D)J recombination-activating protein 2
The deposited structure of PDB entry 6dbw contains 2 copies of Pfam domain PF13341 (RAG2 PHD domain) in V(D)J recombination-activating protein 2. Showing 1 copy in chain B (this domain is out of the observed residue ranges!).

PF03089
Domain description: Recombination activating protein 2
Occurring in:
  1. V(D)J recombination-activating protein 2
The deposited structure of PDB entry 6dbw contains 2 copies of Pfam domain PF03089 (Recombination activating protein 2) in V(D)J recombination-activating protein 2. Showing 1 copy in chain B.

PF12940
Domain description: Recombination-activation protein 1 (RAG1), recombinase
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
The deposited structure of PDB entry 6dbw contains 2 copies of Pfam domain PF12940 (Recombination-activation protein 1 (RAG1), recombinase) in Maltose/maltodextrin-binding periplasmic protein. Showing 1 copy in chain C.

PF00097
Domain description: Zinc finger, C3HC4 type (RING finger)
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
The deposited structure of PDB entry 6dbw contains 2 copies of Pfam domain PF00097 (Zinc finger, C3HC4 type (RING finger)) in Maltose/maltodextrin-binding periplasmic protein. Showing 1 copy in chain C (this domain is out of the observed residue ranges!).

PF01547
Domain description: Bacterial extracellular solute-binding protein
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
The deposited structure of PDB entry 6dbw contains 2 copies of Pfam domain PF01547 (Bacterial extracellular solute-binding protein) in Maltose/maltodextrin-binding periplasmic protein. Showing 1 copy in chain C (this domain is out of the observed residue ranges!).

InterPro InterPro annotations
IPR006060
Domain description: Maltose/Cyclodextrin ABC transporter, substrate-binding protein
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
IPR025162
Domain description: Recombination activating protein 2, PHD domain
Occurring in:
  1. V(D)J recombination-activating protein 2
IPR004321
Domain description: V-D-J recombination activating protein 2
Occurring in:
  1. V(D)J recombination-activating protein 2
IPR001841
Domain description: Zinc finger, RING-type
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
IPR024627
Domain description: V(D)J recombination-activating protein 1
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
IPR011011
Domain description: Zinc finger, FYVE/PHD-type
Occurring in:
  1. V(D)J recombination-activating protein 2
IPR011043
Domain description: Galactose oxidase/kelch, beta-propeller
Occurring in:
  1. V(D)J recombination-activating protein 2
IPR015915
Domain description: Kelch-type beta propeller
Occurring in:
  1. V(D)J recombination-activating protein 2
IPR023336
Domain description: RAG nonamer-binding domain
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
IPR019485
Domain description: V(D)J recombination-activating protein 1, Zinc finger
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
IPR017907
Domain description: Zinc finger, RING-type, conserved site
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
IPR018957
Domain description: Zinc finger, C3HC4 RING-type
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
IPR013083
Domain description: Zinc finger, RING/FYVE/PHD-type
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
IPR006061
Domain description: Solute-binding family 1, conserved site
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1
IPR006059
Domain description: Bacterial-type extracellular solute-binding protein
Occurring in:
  1. Maltose/maltodextrin-binding periplasmic protein; V(D)J recombination-activating protein 1

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