RAG2_DANRE
ID RAG2_DANRE Reviewed; 530 AA.
AC O13034;
DT 15-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-1997, sequence version 1.
DT 03-AUG-2022, entry version 105.
DE RecName: Full=V(D)J recombination-activating protein 2;
DE Short=RAG-2;
GN Name=rag2; Synonyms=rag-2;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND DEVELOPMENTAL STAGE.
RC TISSUE=Larva;
RX PubMed=9089097; DOI=10.1007/s002510050221;
RA Willett C.E., Cherry J.J., Steiner L.A.;
RT "Characterization and expression of the recombination activating genes
RT (rag1 and rag2) of zebrafish.";
RL Immunogenetics 45:394-404(1997).
RN [2]
RP DEVELOPMENTAL STAGE.
RX PubMed=9070331; DOI=10.1006/dbio.1996.8446;
RA Willett C.E., Zapata A.G., Hopkins N., Steiner L.A.;
RT "Expression of zebrafish rag genes during early development identifies the
RT thymus.";
RL Dev. Biol. 182:331-341(1997).
CC -!- FUNCTION: Core component of the RAG complex, a multiprotein complex
CC that mediates the DNA cleavage phase during V(D)J recombination. V(D)J
CC recombination assembles a diverse repertoire of immunoglobulin and T-
CC cell receptor genes in developing B and T lymphocytes through
CC rearrangement of different V (variable), in some cases D (diversity),
CC and J (joining) gene segments. DNA cleavage by the RAG complex occurs
CC in 2 steps: a first nick is introduced in the top strand immediately
CC upstream of the heptamer, generating a 3'-hydroxyl group that can
CC attack the 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. In the RAG complex,
CC rag2 is not the catalytic component but is required for all known
CC catalytic activities mediated by RAG1. It probably acts as a sensor of
CC chromatin state that recruits the RAG complex to H3K4me3 (By
CC similarity). {ECO:0000250}.
CC -!- SUBUNIT: Component of the RAG complex composed of core components rag1
CC and rag2. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- DEVELOPMENTAL STAGE: First detected in the thymus during day 4 of
CC development. Expression then increases in the thymus for at least three
CC weeks. {ECO:0000269|PubMed:9070331, ECO:0000269|PubMed:9089097}.
CC -!- DOMAIN: The atypical PHD-type zinc finger recognizes and binds histone
CC H3 trimethylated on 'Lys-4' (H3K4me3). The atypical PHD-type zinc
CC finger also binds various phosphoinositides (By similarity).
CC {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the RAG2 family. {ECO:0000305}.
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DR EMBL; U71094; AAC60366.1; -; Genomic_DNA.
DR PDB; 3JBW; EM; 4.63 A; B/D=1-530.
DR PDB; 3JBX; EM; 3.40 A; B/D=1-530.
DR PDB; 3JBY; EM; 3.70 A; B/D=1-530.
DR PDB; 6DBI; EM; 3.36 A; B/D=1-530.
DR PDB; 6DBJ; EM; 2.99 A; B/D=1-530.
DR PDB; 6DBL; EM; 5.00 A; B/D=1-530.
DR PDB; 6DBO; EM; 4.45 A; B/D=1-530.
DR PDB; 6DBQ; EM; 4.22 A; B/D=1-530.
DR PDB; 6DBR; EM; 4.00 A; B/D=1-530.
DR PDB; 6DBT; EM; 4.30 A; B/D=1-530.
DR PDB; 6DBU; EM; 3.90 A; B/D=1-530.
DR PDB; 6DBV; EM; 4.29 A; B/D=1-530.
DR PDB; 6DBW; EM; 4.70 A; B/D=1-530.
DR PDB; 6DBX; EM; 4.20 A; B/D=1-530.
DR PDBsum; 3JBW; -.
DR PDBsum; 3JBX; -.
DR PDBsum; 3JBY; -.
DR PDBsum; 6DBI; -.
DR PDBsum; 6DBJ; -.
DR PDBsum; 6DBL; -.
DR PDBsum; 6DBO; -.
DR PDBsum; 6DBQ; -.
DR PDBsum; 6DBR; -.
DR PDBsum; 6DBT; -.
DR PDBsum; 6DBU; -.
DR PDBsum; 6DBV; -.
DR PDBsum; 6DBW; -.
DR PDBsum; 6DBX; -.
DR AlphaFoldDB; O13034; -.
DR SMR; O13034; -.
DR STRING; 7955.ENSDARP00000068402; -.
DR PaxDb; O13034; -.
DR ZFIN; ZDB-GENE-990415-235; rag2.
DR eggNOG; ENOG502QVKU; Eukaryota.
DR InParanoid; O13034; -.
DR PRO; PR:O13034; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Unplaced.
DR GO; GO:0097519; C:DNA recombinase complex; IPI:ZFIN.
DR GO; GO:1905347; C:endodeoxyribonuclease complex; IPI:ZFIN.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003682; F:chromatin binding; ISS:UniProtKB.
DR GO; GO:0035064; F:methylated histone binding; ISS:UniProtKB.
DR GO; GO:0035091; F:phosphatidylinositol binding; ISS:UniProtKB.
DR GO; GO:0005547; F:phosphatidylinositol-3,4,5-trisphosphate binding; ISS:UniProtKB.
DR GO; GO:0043325; F:phosphatidylinositol-3,4-bisphosphate binding; ISS:UniProtKB.
DR GO; GO:0080025; F:phosphatidylinositol-3,5-bisphosphate binding; ISS:UniProtKB.
DR GO; GO:0005546; F:phosphatidylinositol-4,5-bisphosphate binding; ISS:UniProtKB.
DR GO; GO:0043565; F:sequence-specific DNA binding; IPI:ZFIN.
DR GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR GO; GO:0030183; P:B cell differentiation; ISS:UniProtKB.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0048534; P:hematopoietic or lymphoid organ development; IMP:ZFIN.
DR GO; GO:0033152; P:immunoglobulin V(D)J recombination; IDA:ZFIN.
DR GO; GO:0030098; P:lymphocyte differentiation; IMP:ZFIN.
DR GO; GO:0065004; P:protein-DNA complex assembly; IPI:ZFIN.
DR GO; GO:0030217; P:T cell differentiation; IMP:ZFIN.
DR GO; GO:0033077; P:T cell differentiation in thymus; ISS:UniProtKB.
DR GO; GO:0048538; P:thymus development; IMP:ZFIN.
DR GO; GO:0033151; P:V(D)J recombination; IPI:ZFIN.
DR CDD; cd15569; PHD_RAG2; 1.
DR Gene3D; 2.120.10.80; -; 1.
DR InterPro; IPR011043; Gal_Oxase/kelch_b-propeller.
DR InterPro; IPR015915; Kelch-typ_b-propeller.
DR InterPro; IPR004321; RAG2.
DR InterPro; IPR025162; RAG2_PHD.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR PANTHER; PTHR10960; PTHR10960; 1.
DR Pfam; PF03089; RAG2; 1.
DR Pfam; PF13341; RAG2_PHD; 1.
DR SUPFAM; SSF50965; SSF50965; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chromatin regulator; DNA recombination; Metal-binding;
KW Nucleus; Reference proteome; Zinc; Zinc-finger.
FT CHAIN 1..530
FT /note="V(D)J recombination-activating protein 2"
FT /id="PRO_0000167141"
FT ZN_FING 416..485
FT /note="PHD-type; atypical"
FT BINDING 419
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 423
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 446
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 453
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 456
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 459
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 479
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 482
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT STRAND 1..10
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 20..24
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 27..31
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 34..36
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:6DBI"
FT STRAND 45..51
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 54..59
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 106..114
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 120..127
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 130..132
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 141..147
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 150..156
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 159..161
FT /evidence="ECO:0007829|PDB:6DBJ"
FT TURN 164..166
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 169..173
FT /evidence="ECO:0007829|PDB:3JBX"
FT STRAND 175..177
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 182..185
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 187..189
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 191..195
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 209..212
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 215..218
FT /evidence="ECO:0007829|PDB:6DBJ"
FT TURN 224..227
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 233..238
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 242..244
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 247..253
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 263..265
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 267..273
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 277..279
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 287..292
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 300..302
FT /evidence="ECO:0007829|PDB:6DBJ"
FT HELIX 309..313
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 318..323
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 326..332
FT /evidence="ECO:0007829|PDB:6DBJ"
FT STRAND 343..350
FT /evidence="ECO:0007829|PDB:6DBJ"
SQ SEQUENCE 530 AA; 59174 MW; 2E96CD0C3B9F1417 CRC64;
MSLQPLTAVN CGSLVQPGFS LLDLEGDVYL FGQKGWPKRS CPTGIFGVRI KKGELKLRAI
SFSNNSSYLP PLRCPAIAHF EAQDGKPECY LIHGGRTPNN ELSSSLYMLS VDSRGCNRKV
TLRCEEKELV GDVPSARYGH TLSVINSRGK TACVLFGGRS YMPPTERTTQ NWNSVGDCPP
QVYLIDLEFG CCTAHTLPEL TDGQSFHVAL ARQDCVYFLG GHILSSDCRP SRLIRLHVEL
LLGSPVLTCT ILHEGLTITS AIASPIGYHE YIIFGGYQSE TQKRMECTYV GLDDVGVHME
SREPPQWTSE ISHSRTWFGG SLGKGTALVA IPSEGNPTPP EAYHFYQVSF QKEQDGEATA
QGCSQESTDF EDSAPLEDSE ELYFGREPHE LEYSSDVEGD TYNEEDEEDE SQTGYWIKCC
LSCQVDPNIW EPYYSTELTR PAMIFCSRGE GGHWVHAQCM ELPESLLLQL SQDNSKYFCL
DHGGLPKQEM TPPKQMLPVK RVPMKMTHRK APVSLKMTPA KKTFLRRLFD
