ID U3IW73_ANAPP Unreviewed; 1041 AA.
AC U3IW73;
DT 05-JUN-2019, integrated into UniProtKB/TrEMBL.
DT 05-JUN-2019, sequence version 1.
DT 24-JAN-2024, entry version 22.
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:ENSAPLP00000011498.2};
OS Anas platyrhynchos platyrhynchos (Northern mallard).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC Coelurosauria; Aves; Neognathae; Galloanserae; Anseriformes; Anatidae;
OC Anatinae; Anas.
OX NCBI_TaxID=8840 {ECO:0000313|Ensembl:ENSAPLP00000011498.2, ECO:0000313|Proteomes:UP000016666};
RN [1] {ECO:0000313|Ensembl:ENSAPLP00000011498.2, ECO:0000313|Proteomes:UP000016666}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Hou Z.-C., Zhou Z.-K., Zhu F., Hou S.-S.;
RT "A new Pekin duck reference genome.";
RL Submitted (OCT-2017) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|Ensembl:ENSAPLP00000011498.2}
RP IDENTIFICATION.
RG Ensembl;
RL Submitted (SEP-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 AlphaFoldDB; U3IW73; -.
DR STRING; 8840.ENSAPLP00000011498; -.
DR Ensembl; ENSAPLT00000012227.2; ENSAPLP00000011498.2; ENSAPLG00000011756.2.
DR GeneTree; ENSGT00390000008679; -.
DR OMA; WKFKLFK; -.
DR Proteomes; UP000016666; Chromosome 5.
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:0002250; P:adaptive immune response; IEA:Ensembl.
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; IEA:Ensembl.
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; 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}; Reference proteome {ECO:0000313|Proteomes:UP000016666};
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 289..327
FT /note="RING-type"
FT /evidence="ECO:0000259|PROSITE:PS50089"
FT DOMAIN 350..379
FT /note="RAG1-type"
FT /evidence="ECO:0000259|PROSITE:PS51765"
FT DOMAIN 390..457
FT /note="NBD"
FT /evidence="ECO:0000259|PROSITE:PS51487"
FT DNA_BIND 390..457
FT /note="NBD"
FT /evidence="ECO:0000256|PROSITE-ProRule:PRU00820"
SQ SEQUENCE 1041 AA; 119127 MW; 8A5190F3DDA8F1B6 CRC64;
MSIASQMDLP EEIQHPYTKF SEWKFKLFKV RPSEKTSSDN SQCINKDQAE EVASTDKGIM
LHKDEGVPRG EKILTQTDLM GNRQALGKDA NDMKIQDNTE HQNNLKQLCR ICGVSFKSDC
NKRSHPVHGP VDDETLCLLR KKEKKATSWP DLIAKVFKID VRGDVDTIHP TQFCHNCWSI
IHRKFSNTPC EVYFPRNSTM EWQPHSANCD VCHGTSRGVK RKSQLPSVQH GKRVKTIAER
ARVNRGVKNQ AQMNNKNVMK EITNCKNTHL STKLLAVDYP VDFIKSISCQ ICEHILADPV
ETTCRHLFCR TCILKCIKVM GSYCPSCWYP CFPTDLVTPV RSFLNILDSL SIRCPVKECD
EEILHGKYGQ HLSSHKEMKD RELYSHINKG GRPRQHLLSL TRRAQKHRLR ELKCQVKAFA
EKEEGGDIKA VCMTLFLLAL RAKNEHKQAD ELEAIMQGRG SGLHPAVCLA IRVNTFLSCS
QYHKMYRTVK AVSGRQIFQP LHALRTAEKA LLPGYHPFEW KPPLKSVSAN TEVGIIDGLS
GLPLSIDDYP VDTIAKRFRY DTALVSALKD MEEEILEGMK AKNLDDYLSG PFTVVVKESC
DGMGDVSEKH GNGPAVPEKA VRFSFTVMNI SIAHGNEKVR IFEEVKPNSE LCCKPLCLML
ADESDHETLT AILSPLIAER EAMKDSELLL EMGGILRTFK FIFRGTGYDE KLVREVEGLE
ASGSTYICTL CDATRLEASQ NLVFHSITRS HAENLERYEI WRSNPYHESV DELRDRVKGV
SAKPFIETVP SIDALHCDIG NATEFYRIFQ MEIGEVYKNP DVSKEERKRW QLTLDKHLRK
KMNLKPMMRM SGNFARKLMS KETVEAVCEL IKCEERHEAL KELMDLYLKM KPVWRSSCPA
KECPELLCQY SYNSQRFAEL LSTKFKYRYE GKITNYFHKT LAHVPEIIER DGSIGAWASE
GNESGNKLFR RFRKMNARQS KFYEMEDVLK HHWLYTSKYL QKFMNAHKTL RSQGFTIDPE
DSLGDSLPLE VSMESNDSEE L
//
