ID A0A4W6EH50_LATCA Unreviewed; 1071 AA.
AC A0A4W6EH50;
DT 18-SEP-2019, integrated into UniProtKB/TrEMBL.
DT 18-SEP-2019, sequence version 1.
DT 18-JUN-2025, entry version 30.
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};
GN Name=rag1 {ECO:0000313|Ensembl:ENSLCAP00010037034.1,
GN ECO:0000313|RefSeq:XP_018519293.1, ECO:0000313|RefSeq:XP_018519294.1};
OS Lates calcarifer (Barramundi) (Holocentrus calcarifer).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Neoteleostei; Acanthomorphata;
OC Carangaria; Carangaria incertae sedis; Centropomidae; Lates.
OX NCBI_TaxID=8187 {ECO:0000313|Ensembl:ENSLCAP00010037034.1, ECO:0000313|Proteomes:UP000314980};
RN [1] {ECO:0000313|Proteomes:UP000314980}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Sai Rama Sridatta P.;
RL Submitted (SEP-2015) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|Ensembl:ENSLCAP00010037034.1}
RP IDENTIFICATION.
RG Ensembl;
RL Submitted (MAR-2025) to UniProtKB.
RN [3] {ECO:0000313|RefSeq:XP_018519293.1, ECO:0000313|RefSeq:XP_018519294.1}
RP IDENTIFICATION.
RC TISSUE=Brain {ECO:0000313|RefSeq:XP_018519293.1,
RC ECO:0000313|RefSeq:XP_018519294.1};
RG RefSeq;
RL Submitted (MAR-2025) to UniProtKB.
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 RefSeq; XP_018519293.1; XM_018663777.2.
DR RefSeq; XP_018519294.1; XM_018663778.2.
DR AlphaFoldDB; A0A4W6EH50; -.
DR FunCoup; A0A4W6EH50; 642.
DR STRING; 8187.ENSLCAP00010037034; -.
DR Ensembl; ENSLCAT00010037903.1; ENSLCAP00010037034.1; ENSLCAG00010017330.1.
DR GeneID; 108875106; -.
DR KEGG; lcf:108875106; -.
DR CTD; 5896; -.
DR GeneTree; ENSGT00390000008679; -.
DR InParanoid; A0A4W6EH50; -.
DR OrthoDB; 6270329at2759; -.
DR Proteomes; UP000314980; Unassembled WGS sequence.
DR Proteomes; UP000694890; Linkage group LG10.
DR GO; GO:0097519; C:DNA recombinase complex; IEA:TreeGrafter.
DR GO; GO:1905347; C:endodeoxyribonuclease complex; IEA:TreeGrafter.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:1990238; F:double-stranded DNA endonuclease activity; IEA:TreeGrafter.
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:0002250; P:adaptive immune response; IEA:TreeGrafter.
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; 3.30.40.10; 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; 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 SMART; SM00184; RING; 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}; Reference proteome {ECO:0000313|Proteomes:UP000314980};
KW Repeat {ECO:0000256|ARBA:ARBA00022737};
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 313..352
FT /note="RING-type"
FT /evidence="ECO:0000259|PROSITE:PS50089"
FT DOMAIN 374..403
FT /note="RAG1-type"
FT /evidence="ECO:0000259|PROSITE:PS51765"
FT DOMAIN 422..489
FT /note="NBD"
FT /evidence="ECO:0000259|PROSITE:PS51487"
FT DNA_BIND 422..489
FT /note="NBD"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00820"
FT REGION 1..21
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1071 AA; 121557 MW; 2F5EEFAC270EA838 CRC64;
MVEENLETDG PRSSMPAELH HPHSKYAQWK FKLFRVRSME KAPLPGESQP DTGVLLGISP
PAAPKIDLDN GVGPGSVMKL CLGGKSKENV EGPGRRVDKK LQEMDTHMNH LRCLCRLCGV
TLRKVKGPLH EVHGDLDEAS KGALRKMGCK FKSWPEVILK VFKVDVTEDT ESVHPLSFCH
RCWMAAIRGG GFCSFSRIKV PEWKPHSSLC HLCSPKKSSF QRTGRKRRKT IPRAQSLAKR
SRREHADIIA VGERRVLRPF GDRHHGLALR GWRKPSVQRE KWVRNITHCQ KDHLSTKLIS
EKLPVDFLYS FTCLVCDHLL FDPVQSPCGH LFCRSCIIKY NHVLGPHCPA CNLPCAPDDL
TSPAKAFLSA LHSLPLLCPR GGCGEQVRLD SFKAHCLDHE LSEQDANKQS SELDSYLLAN
KGGRPRQHLL SLTRRAQKHR LRDLKNQVKV FADKEEGGDL KSVCQTLFLL ALRSGNEHRQ
ADELEAMMQG RGFGLHPAVC LAIRVNTFLS CSQYHKMYRT VKATSGRQIF QPLHTLRAAE
KELLPGFHQF EWQPALKNVS TSCNVGIING LSGWAASLDD SPADTITRRF RYDVALVSAL
KDLEEDIMEG LRESGMEDSA CTSGFSVMIK ECCDGMGDVS EKHGGGPAVP EKAVRFSFTV
MSVSVLADDD RREVTIFTEP KPNSELSCKP LCLMFVDESD HETLTAVLGP IIAERNAMKE
SRLILPIGGL PRSFRFHFRG TGYDEKMVRE MEGLEASGST YICTLCDSSR AEASQNMVLH
SITRSHEENL ERYEIWRTNP FSESVEELRD RVKGVSAKPF METQPTLDAL HCDIGNATEF
YKIFQDEIGE VYQKVNPSRE ERRSWRAALD KQLRKKMKLK PIMRMNGNYA RRLMTLEAVE
VVCELVPSEE RREALRELMR LYLQMRPVWR ATCPAKECPD QLCRYSFNSQ RFADLLSSTF
KYRYNGKITN YLHKTLAHVP EIIERDGSIG AWASEGNESA NKLFRRFRKM NARQSKAYEL
EDVLKHHWLY TSKYLQKFME AHKDSVKALQ ATIDPVETQD DEDMSLELND F
//
