ID H0ZIP6_TAEGU Unreviewed; 1040 AA.
AC H0ZIP6;
DT 22-FEB-2012, integrated into UniProtKB/TrEMBL.
DT 17-JUN-2020, sequence version 2.
DT 27-MAR-2024, entry version 82.
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:ENSTGUP00000010463.2};
OS Taeniopygia guttata (Zebra finch) (Poephila guttata).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC Coelurosauria; Aves; Neognathae; Passeriformes; Passeroidea; Estrildidae;
OC Estrildinae; Taeniopygia.
OX NCBI_TaxID=59729 {ECO:0000313|Ensembl:ENSTGUP00000010463.2, ECO:0000313|Proteomes:UP000007754};
RN [1] {ECO:0000313|Ensembl:ENSTGUP00000010463.2, ECO:0000313|Proteomes:UP000007754}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=20360741; DOI=10.1038/nature08819;
RA Warren W.C., Clayton D.F., Ellegren H., Arnold A.P., Hillier L.W.,
RA Kunstner A., Searle S., White S., Vilella A.J., Fairley S., Heger A.,
RA Kong L., Ponting C.P., Jarvis E.D., Mello C.V., Minx P., Lovell P.,
RA Velho T.A., Ferris M., Balakrishnan C.N., Sinha S., Blatti C., London S.E.,
RA Li Y., Lin Y.C., George J., Sweedler J., Southey B., Gunaratne P.,
RA Watson M., Nam K., Backstrom N., Smeds L., Nabholz B., Itoh Y., Whitney O.,
RA Pfenning A.R., Howard J., Volker M., Skinner B.M., Griffin D.K., Ye L.,
RA McLaren W.M., Flicek P., Quesada V., Velasco G., Lopez-Otin C.,
RA Puente X.S., Olender T., Lancet D., Smit A.F., Hubley R., Konkel M.K.,
RA Walker J.A., Batzer M.A., Gu W., Pollock D.D., Chen L., Cheng Z.,
RA Eichler E.E., Stapley J., Slate J., Ekblom R., Birkhead T., Burke T.,
RA Burt D., Scharff C., Adam I., Richard H., Sultan M., Soldatov A.,
RA Lehrach H., Edwards S.V., Yang S.P., Li X., Graves T., Fulton L.,
RA Nelson J., Chinwalla A., Hou S., Mardis E.R., Wilson R.K.;
RT "The genome of a songbird.";
RL Nature 464:757-762(2010).
RN [2] {ECO:0000313|Ensembl:ENSTGUP00000010463.2}
RP IDENTIFICATION.
RG Ensembl;
RL Submitted (NOV-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; H0ZIP6; -.
DR STRING; 59729.ENSTGUP00000010463; -.
DR Ensembl; ENSTGUT00000010573.2; ENSTGUP00000010463.2; ENSTGUG00000010147.2.
DR GeneTree; ENSGT00390000008679; -.
DR HOGENOM; CLU_010909_0_0_1; -.
DR InParanoid; H0ZIP6; -.
DR OMA; WKFKLFK; -.
DR OrthoDB; 4577803at2759; -.
DR TreeFam; TF331926; -.
DR Proteomes; UP000007754; 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:UP000007754};
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 1040 AA; 119336 MW; 6FEE8DDA7E8F3671 CRC64;
MSAASQMDLP EELQHTYTKF SEWKFKLFKL RSFEKTPSDD SQHIHKDQAE EAVSSNKEII
LHKDEAVPRG EKTELTGNRQ GLEEDAHAMK TQDIRAHQNN LKQLCRICGV SFKTDCSKRT
YPVHGPVDDE TLYLLRKKEK TATSWPDLIA KVFKTDVRGD VDTIHPTRFC HNCWSIIHRK
FSNTLCEVYF PRNSTMEWQP HSPNCDVCHT TRRGVKRKSQ PPSVQRGKRV KTTVERAQLN
RGVKNQQIKQ AQINNKNLMK EIVNCKDIHL STKLLAIDYP VDFIKSISCQ ICDHILADPV
ETTCRHLFCR TCILKCIRVM GSYCPSCWYP CFPTDLVTPV KSFLNILDNL NIRCPVKECD
EEISHGKYGQ HLSGHKEMKE GELYSYINKG GRPRQHLLSL TRRAQKHRLR ELKRQVKAFA
EKEEGGDIKA VCMTLFLLAL RAKNEHKQAD ELEAIMQGRG SGLHPAVCLA IRINTFLSCS
QYHKMYRTVK AVTGRQIFQP LHALRTAEKA LLPGYHPFEW KPPLKNVSTN TEVGIIDGLS
GLPLSIDDYP VDTIAKRFRY DAALVCALKD MEEEILEGMK AKNLDDYLNG PFTVVVKESC
DGMGDVSEKH GSGPAVPEKA VRFSFTVMNI SIEHGNESKR IFEEVKPNSE LCCKPLCLML
ADESDHETLT AILSPLIAER EAMKNSELLL EMGGILRTFR FVFRGTGYDE KLLREVEGLE
ASGSTYICTL CDATRLEASQ NLVFHSITRS HAENLERYEI WRSNPYHESV DELRDRVKGV
SAKPFIETVP SIDALHCDIG NATEFYRIFQ MEIGELYKNP DVSKEERKRW QLTLDKHLRK
KMNLKPMLKM SGNFARKLMS KETVEAVCEL IKCEERHEAL KELMDLYLKM KPVWRSSCPA
KECPELLCQY SYNSQRFAEL LSTKFKYRYD GKITNYFHKT LAHVPEIIER DGSIGAWASE
GNESGNKLFR RFRKMNARQS KVYEMEDVLK HHWLYTSKYL QKFMNAHKTL KSQSFTIDSG
GSLGDSLLLE VLENSDTAEL
//
