ID C8YKH3_9TYRA Unreviewed; 956 AA.
AC C8YKH3;
DT 03-NOV-2009, integrated into UniProtKB/TrEMBL.
DT 03-NOV-2009, sequence version 1.
DT 13-SEP-2023, entry version 56.
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:ACS74368.1};
OS Phyllomyias uropygialis.
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC Coelurosauria; Aves; Neognathae; Passeriformes; Tyrannidae; Phyllomyias.
OX NCBI_TaxID=360230 {ECO:0000313|EMBL:ACS74368.1};
RN [1] {ECO:0000313|EMBL:ACS74368.1}
RP NUCLEOTIDE SEQUENCE.
RA Tello J.G., Moyle R.G., Marchese D.J., Cracraft J.;
RT "Phylogeny and phylogenetic classification of the tyrant flycatchers,
RT cotingas, manakins, and their allies (Aves: Tyrannides).";
RL Cladistics 25:429-467(2009).
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; FJ501706; ACS74368.1; -; 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}; Coiled coil {ECO:0000256|SAM:Coils};
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 256..294
FT /note="RING-type"
FT /evidence="ECO:0000259|PROSITE:PS50089"
FT DOMAIN 317..346
FT /note="RAG1-type"
FT /evidence="ECO:0000259|PROSITE:PS51765"
FT DOMAIN 357..424
FT /note="NBD"
FT /evidence="ECO:0000259|PROSITE:PS51487"
FT DNA_BIND 357..424
FT /note="NBD"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00820"
FT COILED 36..63
FT /evidence="ECO:0000256|SAM:Coils"
FT NON_TER 1
FT /evidence="ECO:0000313|EMBL:ACS74368.1"
FT NON_TER 956
FT /evidence="ECO:0000313|EMBL:ACS74368.1"
SQ SEQUENCE 956 AA; 109830 MW; 515957FDC4EFF94F CRC64;
KVRSFEKTID DRQHINKDQA EEIASSNKEI ILHKDKAVSR EEKMELMGNR QALEKEAHDM
KTRDNRAHQN NLKQLCRICG VSFKTDCYKR THPVHGPVDD ETLCLLRKKE KKATSWPDLI
AKVFKIDVRG DVDTIHPTRF CHNCWSIIHR KYSSTLCEVY FPRNSTMEWQ XHSPNCDVCH
TTSRGVKRKS QPPSVQHGKR VKTTVERARL NRGVKNQAQI NNKNLMKEIV NCKNIHLSTK
LLAVDYPADF IKSISCQICE HILADPVETT CRHLFCRTCI LKCIKAMGSY CPSCWYPCFP
TDLVTPVKSF LNILDSLGIR CPVKECDEEI LHGKYGQHLS NHKEMKDREL YSYVNKGGRP
RQHLLSLTRR AQKHRLRELK RQVKAFAEKE EGGDIKAVCM TLFLLALRAK NEHRQADELE
AIMQGRGSGL HPAVCLAIRV NTFLSCSQYH KMYRTVKAVT GRQIFQPLHA LRTAEKALLP
GYHPFEWKPP LKNVSTNTEV GIIDGLSGLP LSVDDYPVDT IAKRFRYDAA LVCALKDMEE
EILEGMKAKN LDNYLNGPFT VVIKESCDGM GDVSEKHGSG PAVPEKAVRF SFTIMNIAIA
HGNESKRIFE EVKPNSELCC KPLCLMLADE SDHETLTAIL SPLMAEREAM KNSELLLEMG
GILRTFRFVF RGTGYDEKLV REVEGLEASG STYICTLCDA TRLEASQNLV FHSITRSHAE
NLERYEIWRS NPYHESVDEL RDRVKGVSAK PFIETVPSID ALHCDIGNAT EFYRIFQMEI
GELYKNPDVS KEERKKWQLT LDKHLRKKMN LKPMMKMSGN FARKLMSKEA VEAVCELIKC
EERHEALKEL MDLYLKMKPV WRSSCPAKEC PELLCQYSYN SQRFAELLST KFKYRYEGKI
TNYFHKTLAH VPEIIERDGS IGAWASEGNE SGNKLFRRFR KMNARQSKFY EMEDVL
//
