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Entry: F8UKE2_9SAUR
LinkDB: F8UKE2_9SAUR
Original site: F8UKE2_9SAUR 
ID   F8UKE2_9SAUR            Unreviewed;       574 AA.
AC   F8UKE2;
DT   21-SEP-2011, integrated into UniProtKB/TrEMBL.
DT   21-SEP-2011, sequence version 1.
DT   13-SEP-2023, entry version 46.
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:AEH41989.1};
OS   Nephrurus laevissimus.
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Lepidosauria; Squamata; Bifurcata; Gekkota; Pygopoidea; Carphodactylidae;
OC   Nephrurus.
OX   NCBI_TaxID=1017098 {ECO:0000313|EMBL:AEH41989.1};
RN   [1] {ECO:0000313|EMBL:AEH41989.1}
RP   NUCLEOTIDE SEQUENCE.
RC   STRAIN=SAMAR31893 {ECO:0000313|EMBL:AEH41989.1};
RX   PubMed=21421065; DOI=10.1016/j.ympev.2011.03.018;
RA   Oliver P.M., Bauer A.M.;
RT   "Systematics and evolution of the Australian knob-tail geckos (Nephrurus,
RT   Carphodactylidae, Gekkota): Plesiomorphic grades and biome shifts through
RT   the Miocene.";
RL   Mol. Phylogenet. Evol. 59:664-674(2011).
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; JF807389; AEH41989.1; -; 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};
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          204..243
FT                   /note="RING-type"
FT                   /evidence="ECO:0000259|PROSITE:PS50089"
FT   DOMAIN          265..294
FT                   /note="RAG1-type"
FT                   /evidence="ECO:0000259|PROSITE:PS51765"
FT   DOMAIN          305..372
FT                   /note="NBD"
FT                   /evidence="ECO:0000259|PROSITE:PS51487"
FT   DNA_BIND        305..372
FT                   /note="NBD"
FT                   /evidence="ECO:0000256|PROSITE-ProRule:PRU00820"
FT   NON_TER         1
FT                   /evidence="ECO:0000313|EMBL:AEH41989.1"
FT   NON_TER         574
FT                   /evidence="ECO:0000313|EMBL:AEH41989.1"
SQ   SEQUENCE   574 AA;  65332 MW;  FAC75B33347B9333 CRC64;
     IDKDAFCANQ REIEAHQGNL QQLCRICGGS FKNDPYKRSH PVHGPVDDEM QALLRKKERR
     ATSWPDLLVK VFKTDVRGDI DTIHPTNFCH NCWKVIQRKF SSAPCEVYFP RKGTMEWQPH
     SMNCDVCGTS PHGMKRKKQA LNPQVSKKLR VIAERARKIM HTRSQKPVNS KSLMKKIXNC
     KKIHLXTNML TVDYPADFVK SISCQICEHI LADPVETTCK HLFCRLCILK CLKVIGSYCP
     SCRYPCFPTD LMNPVRSFLN VLNTLVVRCP VKDCHEDVAL GKYSHHFSRH KDNKDKGTYV
     HVNKGGRPRQ HLLSLTRRAQ KHRLRELKLQ VKSFAEKEEG GDVKSVCLTL FLLALRARNE
     HRQADELEAM MQGKGSGLSP SVCLAIRVNT FLSCSQYHKM YRTIKAITGR QIFQPLHALR
     TAEKSLLPGY HPFEWRPPLK NVSSNTEVGI IDGLSGLQHL VDDYPVDTIA KRFRYDSALV
     SALMDMEEDI LEGLMLHDLD DYLKGPFTVV IKESCDGMGD VSEKHGCGPA VPEKAVRFSF
     TLMNITVAHA NENIRIFEEN KPNSELCCKP LCLM
//
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