ID A3FFB5_CALHA Unreviewed; 892 AA.
AC A3FFB5;
DT 20-MAR-2007, integrated into UniProtKB/TrEMBL.
DT 20-MAR-2007, sequence version 1.
DT 13-SEP-2023, entry version 81.
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:ABN50168.1};
OS Calidris himantopus (Stilt sandpiper) (Micropalama himantopus).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC Coelurosauria; Aves; Neognathae; Charadriiformes; Scolopacidae; Calidris.
OX NCBI_TaxID=279938 {ECO:0000313|EMBL:ABN50168.1};
RN [1] {ECO:0000313|EMBL:ABN50168.1}
RP NUCLEOTIDE SEQUENCE.
RX PubMed=17284401; DOI=10.1098/rsbl.2006.0606;
RA Baker A.J., Pereira S.L., Paton T.A.;
RT "Phylogenetic relationships and divergence times of Charadriiformes genera:
RT multigene evidence for the Cretaceous origin of at least 14 clades of
RT shorebirds.";
RL Biol. Lett. 3:205-209(2007).
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; EF373193; ABN50168.1; -; Genomic_DNA.
DR AlphaFoldDB; A3FFB5; -.
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 214..252
FT /note="RING-type"
FT /evidence="ECO:0000259|PROSITE:PS50089"
FT DOMAIN 275..304
FT /note="RAG1-type"
FT /evidence="ECO:0000259|PROSITE:PS51765"
FT DOMAIN 315..382
FT /note="NBD"
FT /evidence="ECO:0000259|PROSITE:PS51487"
FT DNA_BIND 315..382
FT /note="NBD"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00820"
FT REGION 1..22
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..21
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:ABN50168.1"
FT NON_TER 892
FT /evidence="ECO:0000313|EMBL:ABN50168.1"
SQ SEQUENCE 892 AA; 101838 MW; 60A7A7B7C937435F CRC64;
KMDLTGNRQA LEKDVSDMKT QDNKTHQNNL KQLCRICGVS FKADCYKRTH PVHGPVDDET
LWLLRKKEKK ATSWPDLISK VFKIDVRGDV DTVHPTRFCH NCWSIIHRKF SNTPCEVYFP
RNSTMEWQPH SPDCDVCHTT SRGVKRKSQP PSVPHGKRVK SIAERARVNR GAKNQAQINN
KNLMKEIVNC KNTHLSTKLL AVDYPVDFVK SISCQICEHI LADPVETTCR HLFCRTCILK
CIKVMGSYCP SCWYPCFPTD LVTPVKSFLS ILDSLGIRCP VKECDEEVLH GKYGQHLSSH
KEMKDRELCS HINRGGRPRQ HLLSLTRRAQ KHRLRELKRQ VKAFAEKEEG GDIKAVCMTL
FLLALRAKNE HRQADELEAI MRGKGSGLHP AVCLAIRVNT FLSCSQYHKM YRTVKAVTGR
QIFQPLHALR TAEKALLPGY HPFEWKPPLK NVSTNTEVGI IDGLSGLPLS IDDYPVDTIA
KRFRYDAALV CALKDMEEEI LEGMKAKNLD DYLNGPFTVV VKESCDGMGD VSEKHGSGPA
VPEKAVRFSF TVMNIAIACG NESKEIFERV KPNSELCCKP LCLMLADESD HETLTTILSP
LIAEREAMKN SELLLEMGGI LRTLKFIFRG TGYDEKMVRE VEGLEASGST YICTLCDATR
LEASQNLVFH SITRSHAENL ERYEIWRSNP YHEFVDELCD RVKGVSAKPF IETVPSIDAL
HCDIGNATEF YRIFQMEIGE VYKNPDVSKE ERKRWQLTLD KHLRKKMNLK PMMRMSGNFA
RKLMTKETVE AVCELIKCEE RHEALKELMD LYLKMKPVWR SSCPAKECPE LLCQYSYNSQ
RFAELLSTKF KYRYEGKITN YFHKTLAHVP EIIERDGSIG AWASEGNESG NK
//
