ID G3GDL0_BOMBO Unreviewed; 354 AA.
AC G3GDL0;
DT 16-NOV-2011, integrated into UniProtKB/TrEMBL.
DT 16-NOV-2011, sequence version 1.
DT 24-JAN-2024, entry version 52.
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:AEM66132.1};
OS Bombina bombina (Fire-bellied toad).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Bombinatoridae; Bombina.
OX NCBI_TaxID=8345 {ECO:0000313|EMBL:AEM66132.1};
RN [1] {ECO:0000313|EMBL:AEM66132.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Krasno {ECO:0000313|EMBL:AEM66132.1};
RX PubMed=21749513; DOI=10.1111/j.1365-294X.2011.05175.x;
RA Fijarczyk A., Nadachowska K., Hofman S., Litvinchuk S.N., Babik W.,
RA Stuglik M., Gollmann G., Choleva L., Cogalniceanu D., Vukov T., Dzukic G.,
RA Szymura J.M.;
RT "Nuclear and mitochondrial phylogeography of the European fire-bellied
RT toads Bombina bombina and Bombina variegata supports their independent
RT histories.";
RL Mol. Ecol. 20:3381-3398(2011).
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}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|PROSITE-ProRule:PRU00820}.
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DR EMBL; JF898465; AEM66132.1; -; Genomic_DNA.
DR AlphaFoldDB; G3GDL0; -.
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 212..251
FT /note="RING-type"
FT /evidence="ECO:0000259|PROSITE:PS50089"
FT DOMAIN 273..302
FT /note="RAG1-type"
FT /evidence="ECO:0000259|PROSITE:PS51765"
FT DOMAIN 313..354
FT /note="NBD"
FT /evidence="ECO:0000259|PROSITE:PS51487"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:AEM66132.1"
FT NON_TER 354
FT /evidence="ECO:0000313|EMBL:AEM66132.1"
SQ SEQUENCE 354 AA; 40626 MW; 68D11414D5375CF9 CRC64;
PQETNVVEHN KTELIRVEEE VHVAAIQQLC RICGASFKMD QQNRSYPVHG PVDSETQEVL
KRREKKATSW PDLIYKIFKI DVKGDLDIIH PTRFCHNCWI IMNQKFNHNT SEVYFPRNNA
VEWRVHSSDC DVCNTAKIWG KRKGSLQSHS HLPKKCKLGP EFARKNKTSN HPSHGKNNKV
LLQIQTHCKK IHLDSSLLVV DYPSAFIKSV TCQVCEHILS DPVQTTCKHL FCRICILKYI
KLAGCYCPAC RYTCFPTDLT TPVKSYINVL NSLVLKCKIS GCDEETSLGK YHTHISKHTE
SKEKEAYAHI NKGGRPRLHL LSLTRRAQKH RLRELKMQVK AFSDKEEGGD VKSV
//
