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Database: UniProt
Entry: D3YQI2_9PASS
LinkDB: D3YQI2_9PASS
Original site: D3YQI2_9PASS 
ID   D3YQI2_9PASS            Unreviewed;       463 AA.
AC   D3YQI2;
DT   20-APR-2010, integrated into UniProtKB/TrEMBL.
DT   20-APR-2010, sequence version 1.
DT   13-SEP-2023, entry version 58.
DE   RecName: Full=V(D)J recombination-activating protein 1 {ECO:0000256|ARBA:ARBA00021277, ECO:0000256|RuleBase:RU366024};
DE            EC=2.3.2.27 {ECO:0000256|ARBA:ARBA00012483, ECO:0000256|RuleBase:RU366024};
DE            EC=3.1.-.- {ECO:0000256|RuleBase:RU366024};
DE   Flags: Fragment;
GN   Name=RAG-1 {ECO:0000313|EMBL:ADD10804.1};
OS   Dasyornis broadbenti (rufous bristle-bird).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC   Coelurosauria; Aves; Neognathae; Passeriformes; Meliphagoidea;
OC   Dasyornithidae; Dasyornis.
OX   NCBI_TaxID=243059 {ECO:0000313|EMBL:ADD10804.1};
RN   [1] {ECO:0000313|EMBL:ADD10804.1}
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=20152917; DOI=10.1016/j.ympev.2010.02.005;
RA   Gardner J.L., Trueman J.W., Ebert D., Joseph L., Magrath R.D.;
RT   "Phylogeny and evolution of the Meliphagoidea, the largest radiation of
RT   Australasian songbirds.";
RL   Mol. Phylogenet. Evol. 55:1087-1102(2010).
CC   -!- FUNCTION: Catalytic component of the RAG complex, a multiprotein
CC       complex that mediates the DNA cleavage phase during V(D)J
CC       recombination. V(D)J recombination assembles a diverse repertoire of
CC       immunoglobulin and T-cell receptor genes in developing B and T-
CC       lymphocytes through rearrangement of different V (variable), in some
CC       cases D (diversity), and J (joining) gene segments. In the RAG complex,
CC       RAG1 mediates the DNA-binding to the conserved recombination signal
CC       sequences (RSS) and catalyzes the DNA cleavage activities by
CC       introducing a double-strand break between the RSS and the adjacent
CC       coding segment. RAG2 is not a catalytic component but is required for
CC       all known catalytic activities. DNA cleavage occurs in 2 steps: a first
CC       nick is introduced in the top strand immediately upstream of the
CC       heptamer, generating a 3'-hydroxyl group that can attack the
CC       phosphodiester bond on the opposite strand in a direct
CC       transesterification reaction, thereby creating 4 DNA ends: 2 hairpin
CC       coding ends and 2 blunt, 5'-phosphorylated ends.
CC       {ECO:0000256|RuleBase:RU366024}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC         [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC         cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC         EC=2.3.2.27; Evidence={ECO:0000256|ARBA:ARBA00000900,
CC         ECO:0000256|RuleBase:RU366024};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000256|ARBA:ARBA00001946,
CC         ECO:0000256|RuleBase:RU366024};
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000256|RuleBase:RU366024};
CC       Note=Binds 1 divalent metal cation per subunit. Mg(2+) or Mn(2+).
CC       {ECO:0000256|RuleBase:RU366024};
CC   -!- SUBUNIT: Homodimer. {ECO:0000256|RuleBase:RU366024}.
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|PROSITE-ProRule:PRU00820,
CC       ECO:0000256|RuleBase:RU366024}.
CC   -!- DOMAIN: The NBD (nonamer binding) DNA-binding domain mediates the
CC       specific binding to the nonamer RSS motif by forming a tightly
CC       interwoven homodimer that binds and synapses 2 nonamer elements, with
CC       each NBD making contact with both DNA molecules. Each RSS is composed
CC       of well-conserved heptamer (consensus 5'-CACAGTG-3') and nonamer
CC       (consensus 5'-ACAAAAACC-3') sequences separated by a spacer of either
CC       12 bp or 23 bp. {ECO:0000256|PROSITE-ProRule:PRU00820}.
CC   -!- SIMILARITY: Belongs to the RAG1 family. {ECO:0000256|PROSITE-
CC       ProRule:PRU00820, ECO:0000256|RuleBase:RU366024}.
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DR   EMBL; GU825811; ADD10804.1; -; Genomic_DNA.
DR   GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR   GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0042393; F:histone binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0042803; F:protein homodimerization activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0043565; F:sequence-specific DNA binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0061630; F:ubiquitin protein ligase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0030183; P:B cell differentiation; IEA:UniProtKB-UniRule.
DR   GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR   GO; GO:0033077; P:T cell differentiation in thymus; IEA:UniProtKB-UniRule.
DR   GO; GO:0033151; P:V(D)J recombination; IEA:UniProtKB-UniRule.
DR   CDD; cd16530; RING-HC_RAG1; 1.
DR   Gene3D; 6.10.140.510; -; 1.
DR   Gene3D; 3.30.160.60; Classic Zinc Finger; 1.
DR   Gene3D; 3.30.40.10; Zinc/RING finger domain, C3HC4 (zinc finger); 1.
DR   InterPro; IPR024627; RAG1.
DR   InterPro; IPR035714; RAG1_imp-bd.
DR   InterPro; IPR019485; RAG1_Znf.
DR   InterPro; IPR023336; RAG_nonamer-bd_dom.
DR   InterPro; IPR036236; Znf_C2H2_sf.
DR   InterPro; IPR018957; Znf_C3HC4_RING-type.
DR   InterPro; IPR001841; Znf_RING.
DR   InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR   InterPro; IPR017907; Znf_RING_CS.
DR   PANTHER; PTHR11539:SF0; V(D)J RECOMBINATION-ACTIVATING PROTEIN 1; 1.
DR   PANTHER; PTHR11539; VDJ RECOMBINATION ACTIVATING PROTEIN 1 RAG1; 1.
DR   Pfam; PF12940; RAG1; 1.
DR   Pfam; PF12560; RAG1_imp_bd; 1.
DR   Pfam; PF00097; zf-C3HC4; 1.
DR   Pfam; PF10426; zf-RAG1; 1.
DR   SMART; SM00184; RING; 1.
DR   SUPFAM; SSF57667; beta-beta-alpha zinc fingers; 1.
DR   SUPFAM; SSF57850; RING/U-box; 1.
DR   PROSITE; PS51487; NBD; 1.
DR   PROSITE; PS51765; ZF_RAG1; 1.
DR   PROSITE; PS00518; ZF_RING_1; 1.
DR   PROSITE; PS50089; ZF_RING_2; 1.
PE   3: Inferred from homology;
KW   Chromatin regulator {ECO:0000256|ARBA:ARBA00022853,
KW   ECO:0000256|RuleBase:RU366024};
KW   DNA recombination {ECO:0000256|ARBA:ARBA00023172, ECO:0000256|PROSITE-
KW   ProRule:PRU00820};
KW   DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|PROSITE-
KW   ProRule:PRU00820};
KW   Endonuclease {ECO:0000256|ARBA:ARBA00022759,
KW   ECO:0000256|RuleBase:RU366024};
KW   Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|RuleBase:RU366024};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723,
KW   ECO:0000256|RuleBase:RU366024};
KW   Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268,
KW   ECO:0000256|RuleBase:RU366024};
KW   Nuclease {ECO:0000256|ARBA:ARBA00022722, ECO:0000256|RuleBase:RU366024};
KW   Nucleus {ECO:0000256|ARBA:ARBA00023242, ECO:0000256|PROSITE-
KW   ProRule:PRU00820};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|RuleBase:RU366024};
KW   Ubl conjugation pathway {ECO:0000256|ARBA:ARBA00022786,
KW   ECO:0000256|RuleBase:RU366024};
KW   Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|RuleBase:RU366024};
KW   Zinc-finger {ECO:0000256|ARBA:ARBA00022771, ECO:0000256|PROSITE-
KW   ProRule:PRU01101}.
FT   DOMAIN          233..271
FT                   /note="RING-type"
FT                   /evidence="ECO:0000259|PROSITE:PS50089"
FT   DOMAIN          294..323
FT                   /note="RAG1-type"
FT                   /evidence="ECO:0000259|PROSITE:PS51765"
FT   DOMAIN          334..401
FT                   /note="NBD"
FT                   /evidence="ECO:0000259|PROSITE:PS51487"
FT   DNA_BIND        334..401
FT                   /note="NBD"
FT                   /evidence="ECO:0000256|PROSITE-ProRule:PRU00820"
FT   NON_TER         1
FT                   /evidence="ECO:0000313|EMBL:ADD10804.1"
FT   NON_TER         463
FT                   /evidence="ECO:0000313|EMBL:ADD10804.1"
SQ   SEQUENCE   463 AA;  53264 MW;  B5432AB1C4C30F17 CRC64;
     ASSNKEFILH KDEAVPRGEK MKLMGNRQEL EEDAHAVKTQ DNRAHQNNLK QLCRICGVSF
     KTDCYKSTYP VHGPVDDETL WLLRKKEKTA TSWPDLIAKV FKIDVRGDVD TIHPTRFCHN
     CWSIIHRKFS NTLCEVYFPR NSTMDWQPHS PNCDVCHTTR RGVKRKSQLP SVQRSKRVKT
     TGERAQLNRG VKNQAQINNK NVMKEIVNCX DIHLSTKLLA VDYPVDFIKS ISCQICEHIL
     ADPVETTCRH LFCRACILKC IRVMGSYCPS CWYPCFPTDL VTPVKSFLNI LDNLSIRCPV
     KECDEEISHG KYGQHLSSHK EMKDRELYSY INKGGRPRQH LLSLTRRAQK HRLRELKRQV
     KAFAEKEEGG DIKAVCMTLF LLALRAKNEH KQADELEAIM QGRGSGLHPA VCLAIRVNTF
     LSCSQYHKMY RTVKAVTGRQ IFQPLHALRM AEKALLPGYH PFE
//
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