ID F1MG60_BOVIN Unreviewed; 1043 AA.
AC F1MG60;
DT 03-MAY-2011, integrated into UniProtKB/TrEMBL.
DT 16-NOV-2011, sequence version 2.
DT 24-JAN-2024, entry version 86.
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:ENSBTAP00000048319.2,
GN ECO:0000313|VGNC:VGNC:33693};
OS Bos taurus (Bovine).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC Bovinae; Bos.
OX NCBI_TaxID=9913 {ECO:0000313|Ensembl:ENSBTAP00000048319.2, ECO:0000313|Proteomes:UP000009136};
RN [1] {ECO:0000313|Ensembl:ENSBTAP00000048319.2, ECO:0000313|Proteomes:UP000009136}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Hereford {ECO:0000313|Ensembl:ENSBTAP00000048319.2,
RC ECO:0000313|Proteomes:UP000009136};
RA Rosen B.D., Bickhart D.M., Koren S., Schnabel R.D., Hall R., Zimin A.,
RA Dreischer C., Schultheiss S., Schroeder S.G., Elsik C.G., Couldrey C.,
RA Liu G.E., Van Tassell C.P., Phillippy A.M., Smith T.P.L., Medrano J.F.;
RT "ARS-UCD1.2.";
RL Submitted (MAR-2018) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|Ensembl:ENSBTAP00000048319.2}
RP IDENTIFICATION.
RC STRAIN=Hereford {ECO:0000313|Ensembl:ENSBTAP00000048319.2};
RG Ensembl;
RL Submitted (JUL-2023) 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_010811097.1; XM_010812795.1.
DR RefSeq; XP_010821203.1; XM_010822901.2.
DR AlphaFoldDB; F1MG60; -.
DR SMR; F1MG60; -.
DR STRING; 9913.ENSBTAP00000048319; -.
DR PaxDb; 9913-ENSBTAP00000048319; -.
DR Ensembl; ENSBTAT00000055549.3; ENSBTAP00000048319.2; ENSBTAG00000040293.3.
DR VEuPathDB; HostDB:ENSBTAG00000040293; -.
DR VGNC; VGNC:33693; RAG1.
DR eggNOG; ENOG502QSFV; Eukaryota.
DR GeneTree; ENSGT00390000008679; -.
DR HOGENOM; CLU_010909_0_0_1; -.
DR InParanoid; F1MG60; -.
DR OMA; WKFKLFK; -.
DR TreeFam; TF331926; -.
DR Proteomes; UP000009136; Chromosome 15.
DR Bgee; ENSBTAG00000040293; Expressed in thymus and 8 other cell types or tissues.
DR GO; GO:0097519; C:DNA recombinase complex; IBA:GO_Central.
DR GO; GO:1905347; C:endodeoxyribonuclease complex; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
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; IBA:GO_Central.
DR GO; GO:0061630; F:ubiquitin protein ligase activity; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0002250; P:adaptive immune response; IBA:GO_Central.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0070244; P:negative regulation of thymocyte apoptotic process; IEA:Ensembl.
DR GO; GO:0045582; P:positive regulation of T cell differentiation; IEA:Ensembl.
DR GO; GO:0002331; P:pre-B cell allelic exclusion; IBA:GO_Central.
DR GO; GO:0051865; P:protein autoubiquitination; IEA:Ensembl.
DR GO; GO:0033077; P:T cell differentiation in thymus; IEA:UniProtKB-UniRule.
DR GO; GO:0043029; P:T cell homeostasis; IEA:Ensembl.
DR GO; GO:0048538; P:thymus development; IEA:Ensembl.
DR GO; GO:0033151; P:V(D)J recombination; IBA:GO_Central.
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}; Reference proteome {ECO:0000313|Proteomes:UP000009136};
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 293..332
FT /note="RING-type"
FT /evidence="ECO:0000259|PROSITE:PS50089"
FT DOMAIN 354..383
FT /note="RAG1-type"
FT /evidence="ECO:0000259|PROSITE:PS51765"
FT DOMAIN 392..459
FT /note="NBD"
FT /evidence="ECO:0000259|PROSITE:PS51487"
FT DNA_BIND 392..459
FT /note="NBD"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00820"
FT REGION 39..97
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 39..55
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1043 AA; 118830 MW; 327CECFFACAA0031 CRC64;
MAVSLPPTLG LSSAPDEIQH PHIKFSEWKF KLFRVRSFEK APENAQAEKQ DSSEGKPSLE
QSPAALDKVG GPKPALTQPV LKPHPKFQKK SHDDGKARDK AIHQANLRHL CRICGNSLKA
DQHHRRYPVH GPVDGKTQVL LRKKEKRATS WPDLIAKVFR IDVKADVDSI HPTEFCHNCW
SFMHRKFSSA PREVYSSRNA TMEWHPHTPS CDICDAARRG LKRKSQPPNS QLSKRLRTVI
DRARQARRCK RRTQDRISSK ELMKKTTNCS KIHLSTRLLA VDFPAHFVKS ISCQICEHIL
ADPVETNCKH VFCRICILRC LKVLGSYCPS CQYPCFPTDL ESPVKSFLSI LNSLMVKCPA
EECDEEVSLE KYNHHVSSHK ESKETFVHIN KGGRPRQHLL SLTRRAQKHR LRELKMQVKA
FADKEEGGDV KSVCLTLFLL ALRARNEHRQ ADELEAIMKG RGSGLQPAVC LAIRVNTFLS
CSQYHKMYRT VKAITGRQIF QPLHSLRSAE KVLLPGYHPF EWQPPLKNVS SSTDVGIIDG
LSGLASSVDD YPVDTIAKRF RYDAALVSAL MDMEEDILEG MRARELDDYL NGPFTVVVKE
SCDGMGDVSE KHGSGPAVPE KAVRFSFTVM KISVAHGSQN VKVFEEAKPN SELCCKPLCL
MLADESDHET LTAILSPLIA EREAMKSSEL MLEMGGILRT FKFIFRGTGY DEKLVREVEG
LEASGSVYIC TLCDATRLEA SQNLVFHSIT RSHAENLERY EVWRSNPYHE TVEELRDRVK
GVSAKPFIET VPSIDALHCD IGNAAEFYKI FQLEIGEVYK NPNASKEERK RWQATLDKHL
RKKMNLKPIM RMNGNFARKL MTKETVEAVC ELIPSQERHE ALKELMDLYL KMKPVWRSSC
PAKECPESLC QYSFNSQRFA ELLSTKFKYR YEGKITNYFH KTLAHVPEII ERDGSIGAWA
SEGNESGNKL FRRFRKMNAR QSKYYEMEDV LKHHWLYTSK YLQKFMNAHN ALKDSGFTLN
SQGGLGDLLD LEESPESQDS MEF
//