Q5NJW5 · Q5NJW5_9AVES

Function

function

Catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell receptor genes in developing B and T-lymphocytes through rearrangement of different V (variable), in some cases D (diversity), and J (joining) gene segments. In the RAG complex, RAG1 mediates the DNA-binding to the conserved recombination signal sequences (RSS) and catalyzes the DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. RAG2 is not a catalytic component but is required for all known catalytic activities. DNA cleavage occurs in 2 steps: a first nick is introduced in the top strand immediately upstream of the heptamer, generating a 3'-hydroxyl group that can attack the phosphodiester bond on the opposite strand in a direct transesterification reaction, thereby creating 4 DNA ends: 2 hairpin coding ends and 2 blunt, 5'-phosphorylated ends.

Catalytic activity

  • S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6-ubiquitinyl-[acceptor protein]-L-lysine.
    EC:2.3.2.27 (UniProtKB | ENZYME | Rhea)

Cofactor

Protein has several cofactor binding sites:
Mg2+ (UniProtKB | Rhea| CHEBI:18420 )

Mn2+ (UniProtKB | Rhea| CHEBI:29035 )

Note: Binds 1 divalent metal cation per subunit. Mg2+ or Mn2+.

Features

Showing features for dna binding.

TypeIDPosition(s)Description
DNA binding358-425NBD

GO annotations

AspectTerm
Cellular ComponentDNA recombinase complex
Cellular Componentendodeoxyribonuclease complex
Cellular Componentnucleus
Molecular Functiondouble-stranded DNA endonuclease activity
Molecular Functionhistone binding
Molecular Functionprotein homodimerization activity
Molecular Functionsequence-specific DNA binding
Molecular Functionubiquitin protein ligase activity
Molecular Functionzinc ion binding
Biological Processadaptive immune response
Biological Processchromatin organization
Biological Processpre-B cell allelic exclusion
Biological ProcessT cell differentiation in thymus
Biological ProcessV(D)J recombination

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    V(D)J recombination-activating protein 1
  • EC number

Gene names

    • Name
      rag-1

Organism names

  • Taxonomic identifier
  • Taxonomic lineage
    Eukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Archelosauria > Archosauria > Dinosauria > Saurischia > Theropoda > Coelurosauria > Aves > Neognathae > Neoaves > Telluraves > Accipitrimorphae > Accipitriformes > Accipitridae > Accipitrinae > Aquila

Accessions

  • Primary accession
    Q5NJW5

Subcellular Location

Keywords

  • Cellular component

Interaction

Subunit

Homodimer.

Family & Domains

Features

Showing features for region, domain.

TypeIDPosition(s)Description
Region1-41Disordered
Domain257-295RING-type
Domain318-347RAG1-type
Domain358-425NBD

Domain

The NBD (nonamer binding) DNA-binding domain mediates the specific binding to the nonamer RSS motif by forming a tightly interwoven homodimer that binds and synapses 2 nonamer elements, with each NBD making contact with both DNA molecules. Each RSS is composed of well-conserved heptamer (consensus 5'-CACAGTG-3') and nonamer (consensus 5'-ACAAAAACC-3') sequences separated by a spacer of either 12 bp or 23 bp.

Sequence similarities

Belongs to the RAG1 family.

Keywords

Family and domain databases

Sequence

  • Sequence status
    Fragment
  • Length
    659
  • Mass (Da)
    74,834
  • Last updated
    2005-02-01 v1
  • Checksum
    8202B76EAAE0D7FE
KVRSFEKRLSDDSQHINKDQAEEVTSSSKEIILHKDEAVPRGEKMDLMGNRQALEKDANDMQTEDNKAHQNNLKQLCRICGVSFKTDCYKRTHPVHGPVDDETLWLLRKKEKKATSWPDLIAKVFKIDVRGDVDTIHPTQFCHNCWSIIHRKFSNTPCEVYFPRNSTMEWQPHSPNCAVCHTTRRGVKRKSQPPSVQHGKRVKTIAERARINRGVKNQAQINNKNLMKEIVNCKNIHLSTKLLAVDYPVDFIKSISCQICEHILADPVETTCRHLFCRTCILKCIKVMGSYCPSCWYPCFPTDLVTPVKSFLNILDSLGIRCPVKECDEEILHGKYGQHLSSHKEMKESEPYNHVNKGGRPRQHLLSLTRRAQKHRLRELKRQVKAFAEKEEGGDIKAVCMTLFLLALRAKNEHRQADELEAIMQGRGSGLHPAVCLAIRVNTFLSCSQYHKMYRTVKAVTGRQIFQPLHALRTAEKALLPGYHPFEWKPPLKNVSTNTEVGIIDGLSGLPLSIDDYPVDTIAKRFRYDAALVCALKDMEEEILEGMKAKNLDDYLNGPFTVVVKESCDGMGDVSEKHGNGPAVPEKAVRFSFTVMNIAIAHGNESKRIFEEVKPNSQLCCKPLCLMLADESDHETLTAILSPLIAEREAMKNSELLLE

Features

Showing features for non-terminal residue.

TypeIDPosition(s)Description
Non-terminal residue1
Non-terminal residue659

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
AJ601457
EMBL· GenBank· DDBJ
CAE53130.2
EMBL· GenBank· DDBJ
Genomic DNA

Similar Proteins

Disclaimer

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