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Entry: Q5MPL7_LEIBE
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Original site: Q5MPL7_LEIBE 
ID   Q5MPL7_LEIBE            Unreviewed;       945 AA.
AC   Q5MPL7;
DT   01-FEB-2005, integrated into UniProtKB/TrEMBL.
DT   01-FEB-2005, sequence version 1.
DT   13-SEP-2023, 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};
DE   Flags: Fragment;
GN   Name=RAG-1 {ECO:0000313|EMBL:AAV90765.1};
OS   Leiolepis belliana (Common butterfly lizard).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Lepidosauria; Squamata; Bifurcata; Unidentata; Episquamata; Toxicofera;
OC   Iguania; Acrodonta; Agamidae; Leiolepinae; Leiolepis.
OX   NCBI_TaxID=52196 {ECO:0000313|EMBL:AAV90765.1};
RN   [1] {ECO:0000313|EMBL:AAV90765.1}
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=15545252; DOI=10.1080/10635150490522340;
RA   Townsend T., Larson A., Louis E., Macey J.R.;
RT   "Molecular phylogenetics of squamata: the position of snakes,
RT   amphisbaenians, and dibamids, and the root of the squamate tree.";
RL   Syst. Biol. 53:735-757(2004).
RN   [2] {ECO:0000313|EMBL:AAV90765.1}
RP   NUCLEOTIDE SEQUENCE.
RA   Townsend T.M., Larson A.L., Louis E., Macey J.R.;
RL   Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
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; AY662587; AAV90765.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q5MPL7; -.
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          262..300
FT                   /note="RING-type"
FT                   /evidence="ECO:0000259|PROSITE:PS50089"
FT   DOMAIN          323..352
FT                   /note="RAG1-type"
FT                   /evidence="ECO:0000259|PROSITE:PS51765"
FT   DOMAIN          363..430
FT                   /note="NBD"
FT                   /evidence="ECO:0000259|PROSITE:PS51487"
FT   DNA_BIND        363..430
FT                   /note="NBD"
FT                   /evidence="ECO:0000256|PROSITE-ProRule:PRU00820"
FT   REGION          1..43
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   NON_TER         1
FT                   /evidence="ECO:0000313|EMBL:AAV90765.1"
FT   NON_TER         945
FT                   /evidence="ECO:0000313|EMBL:AAV90765.1"
SQ   SEQUENCE   945 AA;  107517 MW;  F105EBF34DBFFA6A CRC64;
     KVRPLGKPFP EDSHLANSNK GEVADSLDKV TEKQAEVPAL PSQVPSEIDT ELNRSIQTIS
     KDAFILSQRE IENHQANLQN LCRICGGAFK SDPYKRSYPV HGPVDDDTQA LLRKKEKRAT
     SWPDLLAKVF KIDVRGDLDT IHPTNFCHNC WNVIQRKFSN SPSEVYFPRK GTMEWHPHSL
     SCDVCGTSFR GVKRKKRSLN PPLNKKPRIV AGCARKIRHV RNVKQVSNKS VMKKIANCKK
     IHLSTKILAV DYPVDFVKAI SCQVCEHILA DPVETTCKHL FCRACILKCI KVMGSYCPAC
     LYPCFPTDLV SPVKSFLNIL NSLVLKCPLK DCQEEVILGK YCHHFNNHKE AEDKEGYVFI
     NKGGRPRQHL LSLTRRAQKH RLRELKLQVK AFAEKEEGGD VKSVCLTLFL LALRARNEHR
     QADELEAIMQ GKGSGLHPAV CLAIRVNTFL SCSQYHKMYR TVKAITGRQI FQPLHALRTA
     EKSLLPGYYP FEWKPPLKNV SSNTNVGIID GLSGIQHLVD DYPVDTIAKR FRYDAALVSA
     LMDMEEDILE GLKTQDLDDY LKGPFTVVIK ESCDGMGDVS EKHGCGPAVP EKAVRFSFTL
     MRISVAHNDG NVKIFEENKP NSELCCKPLC LMLADESDHE TLTAILSPLV AEREAMKNSV
     LILDMAGIPR MFKFVFRGTG YDEKLVREVE GLEASGSTYI CTLCDTTRQE ASQNLILHSI
     TRSHAENLER YEVWRSNPYH ETVDELRDRV KGVSAKPFIE TVPSIDALHC DIGNAAEFYK
     IFQFEIGQVY KNSNASKEER KRWQSTLDKH LRKKMNLKPV LRMNGNFARK LMTKETVEAV
     CELIKCEERQ EALRELMDLY LKMKPVWRTS CPTKECPELV CQYSFHSQRF AELLSTKFRY
     RYEGKITNYF HKTLAHVPEI IERDGSIGAW ASEGNESGNK LFRRF
//
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