UniProtKB - O13033 (RAG1_DANRE)
V(D)J recombination-activating protein 1
rag1
Functioni
Catalytic component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell receptor genes in developing B and T lymphocytes through rearrangement of different V (variable), in some cases D (diversity), and J (joining) gene segments. In the RAG complex, RAG1 mediates the DNA-binding to the conserved recombination signal sequences (RSS) and catalyzes the DNA cleavage activities by introducing a double-strand break between the RSS and the adjacent coding segment. RAG2 is not a catalytic component but is required for all known catalytic activities. DNA cleavage occurs in 2 steps: a first nick is introduced in the top strand immediately upstream of the heptamer, generating a 3'-hydroxyl group that can attack the phosphodiester bond on the opposite strand in a direct transesterification reaction, thereby creating 4 DNA ends: 2 hairpin coding ends and 2 blunt, 5'-phosphorylated ends. In addition to its endonuclease activity, RAG1 also acts as an E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3. Histone H3 monoubiquitination is required for the joining step of V(D)J recombination (By similarity).
By similarityCatalytic activityi
- S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine. EC:2.3.2.27
Cofactori
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 272 | Zinc 1By similarity | 1 | |
Metal bindingi | 276 | Zinc 1By similarity | 1 | |
Metal bindingi | 296 | Zinc 2By similarity | 1 | |
Metal bindingi | 299 | Zinc 1By similarity | 1 | |
Metal bindingi | 299 | Zinc 2By similarity | 1 | |
Metal bindingi | 301 | Zinc 1By similarity | 1 | |
Metal bindingi | 311 | Zinc 3By similarity | 1 | |
Metal bindingi | 313 | Zinc 3By similarity | 1 | |
Metal bindingi | 316 | Zinc 2By similarity | 1 | |
Metal bindingi | 319 | Zinc 2By similarity | 1 | |
Metal bindingi | 331 | Zinc 3By similarity | 1 | |
Metal bindingi | 334 | Zinc 3By similarity | 1 | |
Metal bindingi | 361 | Zinc 4PROSITE-ProRule annotation | 1 | |
Metal bindingi | 366 | Zinc 4PROSITE-ProRule annotation | 1 | |
Metal bindingi | 378 | Zinc 4PROSITE-ProRule annotation | 1 | |
Metal bindingi | 382 | Zinc 4PROSITE-ProRule annotation | 1 | |
Metal bindingi | 620 | Divalent metal cation; catalyticBy similarity | 1 | |
Metal bindingi | 730 | Divalent metal cation; catalyticBy similarity | 1 | |
Sitei | 915 | Essential for DNA hairpin formation, participates in base-stacking interactions near the cleavage siteBy similarity | 1 | |
Metal bindingi | 984 | Divalent metal cation; catalyticBy similarity | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 296 – 335 | RING-typePROSITE-ProRule annotationAdd BLAST | 40 | |
Zinc fingeri | 357 – 386 | RAG1-typePROSITE-ProRule annotationAdd BLAST | 30 | |
DNA bindingi | 408 – 475 | NBDPROSITE-ProRule annotationAdd BLAST | 68 |
GO - Molecular functioni
- endonuclease activity Source: UniProtKB
- histone binding Source: UniProtKB
- magnesium ion binding Source: ZFIN
- metal ion binding Source: UniProtKB
- protein homodimerization activity Source: UniProtKB
- sequence-specific DNA binding Source: ZFIN
- ubiquitin protein ligase activity Source: GO_Central
- ubiquitin-protein transferase activity Source: UniProtKB
- zinc ion binding Source: UniProtKB
GO - Biological processi
- adaptive immune response Source: GO_Central
- B cell differentiation Source: UniProtKB
- chromatin organization Source: UniProtKB-KW
- histone monoubiquitination Source: UniProtKB
- protein-DNA complex assembly Source: ZFIN
- somatic diversification of immune receptors via germline recombination within a single locus Source: ZFIN
- T cell differentiation in thymus Source: UniProtKB
- V(D)J recombination Source: ZFIN
Keywordsi
Molecular function | Chromatin regulator, DNA-binding, Endonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Transferase |
Biological process | DNA recombination, Ubl conjugation pathway |
Ligand | Metal-binding, Zinc |
Names & Taxonomyi
Protein namesi | |
Gene namesi | Name:rag1 |
Organismi | Danio rerio (Zebrafish) (Brachydanio rerio) |
Taxonomic identifieri | 7955 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Actinopterygii › Neopterygii › Teleostei › Ostariophysi › Cypriniformes › Danionidae › Danioninae › Danio |
Proteomesi |
|
Organism-specific databases
ZFINi | ZDB-GENE-990415-234, rag1 |
Subcellular locationi
Nucleus
- Nucleus PROSITE-ProRule annotation
Nucleus
- nucleus Source: UniProtKB
Other locations
- DNA recombinase complex Source: ZFIN
- endodeoxyribonuclease complex Source: ZFIN
Keywords - Cellular componenti
NucleusPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000056009 | 1 – 1057 | V(D)J recombination-activating protein 1Add BLAST | 1057 |
Proteomic databases
PaxDbi | O13033 |
Expressioni
Tissue specificityi
Developmental stagei
Interactioni
Subunit structurei
Homodimer.
Component of the RAG complex composed of core components rag1 and rag2 (By similarity).
By similarityGO - Molecular functioni
- histone binding Source: UniProtKB
- protein homodimerization activity Source: UniProtKB
Protein-protein interaction databases
STRINGi | 7955.ENSDARP00000120100 |
Structurei
Secondary structure
3D structure databases
SMRi | O13033 |
ModBasei | Search... |
PDBe-KBi | Search... |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 1 – 21 | DisorderedSequence analysisAdd BLAST | 21 | |
Regioni | 39 – 61 | DisorderedSequence analysisAdd BLAST | 23 |
Domaini
Sequence similaritiesi
Zinc finger
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 296 – 335 | RING-typePROSITE-ProRule annotationAdd BLAST | 40 | |
Zinc fingeri | 357 – 386 | RAG1-typePROSITE-ProRule annotationAdd BLAST | 30 |
Keywords - Domaini
Zinc-fingerPhylogenomic databases
eggNOGi | ENOG502QSFV, Eukaryota |
InParanoidi | O13033 |
OrthoDBi | 85196at2759 |
PhylomeDBi | O13033 |
Family and domain databases
Gene3Di | 3.30.40.10, 1 hit |
InterProi | View protein in InterPro IPR024627, RAG1 IPR035714, RAG1_imp-bd IPR019485, RAG1_Znf IPR023336, RAG_nonamer-bd_dom IPR018957, Znf_C3HC4_RING-type IPR001841, Znf_RING IPR013083, Znf_RING/FYVE/PHD IPR017907, Znf_RING_CS |
PANTHERi | PTHR11539, PTHR11539, 1 hit |
Pfami | View protein in Pfam PF12940, RAG1, 1 hit PF12560, RAG1_imp_bd, 1 hit PF00097, zf-C3HC4, 1 hit |
SMARTi | View protein in SMART SM00184, RING, 1 hit |
PROSITEi | View protein in PROSITE PS51487, NBD, 1 hit PS51765, ZF_RAG1, 1 hit PS00518, ZF_RING_1, 1 hit PS50089, ZF_RING_2, 1 hit |
(1+)i Sequence
Sequence statusi: Complete.
This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.Show allAlign All
10 20 30 40 50
MEKGRWSSED APRASMPDEL SHPKFSEWKF KLFRVRSMEK APVQNETPVE
60 70 80 90 100
KENQPELAME KTSSQGSVMR LCFGGKSKEN VESARGRVDL KLQEIDTHMN
110 120 130 140 150
LLKNMCRLCG IAIQKAKGPS HEVQGVLEES SRCALRRMGC KLVTWPEVIL
160 170 180 190 200
KVFKVDVTTD METVHPSLFC HRCWTAAIRG GGFCSFTNTR IPDWKPHTSQ
210 220 230 240 250
CNLCFPKKSS FQRVGRKRTK PLKSAHILPK RFRRDSSESS RVWRQTTENP
260 270 280 290 300
DGKEWLKLSV QRGQWVKNIT RCQRDHLSTK LIPTEVPADL IRAVTCQVCD
310 320 330 340 350
HLLSDPVQSP CRHLFCRLCI IRYTHALGPN CPTCNQHLNP SHLIKPAKFF
360 370 380 390 400
LATLSSLPLL CPSEECSDWV RLDSFREHCL NHYREKESQE EQTPSEQNLD
410 420 430 440 450
GYLPVNKGGR PRQHLLSLTR RAQKHRLRDL KNQVKTFAEK EEGGDVKSVC
460 470 480 490 500
LTLFLLALRA GNEHKQADEL EAMMQGRGFG LHPAVCLAIR VNTFLSCSQY
510 520 530 540 550
HKMYRTVKAT SGRQIFQPLH TLRNAEKELL PGFHQFEWQP ALKNVSTSWD
560 570 580 590 600
VGIIDGLSGW TVSVDDVPAD TISRRFRYDV ALVSALKDLE EDIMEGLRER
610 620 630 640 650
ALDDSMCTSG FTVVVKESCD GMGDVSEKHG SGPAVPEKAV RFSFTIMSIS
660 670 680 690 700
IRLEGEDDGI TIFQEQKPNS ELSCRPLCLM FVDESDHETL TAILGPVVAE
710 720 730 740 750
RKAMMESRLI ISVGGLLRSF RFFFRGTGYD EKMVREMEGL EASGSTYICT
760 770 780 790 800
LCDSTRAEAS QNMVLHSITR SHDENLERYE IWRKNPFSES ADELRDRVKG
810 820 830 840 850
VSAKPFMETQ PTLDALHCDI GNATEFYKIF QDEIGEVYQK PNPSREERRR
860 870 880 890 900
WRSTLDKQLR KKMKLKPVMR MNGNYARRLM TREAVEAVCE LVPSEERREA
910 920 930 940 950
LLKLMDLYLQ MKPVWRSTCP SRDCPDQLCQ YSYNSQQFAD LLSSMFKYRY
960 970 980 990 1000
DGKITNYLHK TLAHVPEIVE RDGSIGAWAS EGNESGNKLF RRFRKMNARQ
1010 1020 1030 1040 1050
SKTFELEDIL KHHWLYTSKY LQKFMEAHKN SVKAMQATFN PEETPEEADN
SLDVPDF
Computationally mapped potential isoform sequencesi
There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basketF1QD74 | F1QD74_DANRE | V(D)J recombination-activating prot... | rag1 | 1,057 | Annotation score: | ||
A0A2R8PY29 | A0A2R8PY29_DANRE | V(D)J recombination-activating prot... | rag1 | 1,016 | Annotation score: |
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 895 | E → A in AAA62611 (PubMed:7806278).Curated | 1 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | U71093 Genomic DNA Translation: AAC60365.1 U13983 Genomic DNA Translation: AAA62611.1 |
PIRi | I50115 |
RefSeqi | NP_571464.1, NM_131389.1 |
Genome annotation databases
GeneIDi | 30663 |
KEGGi | dre:30663 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | U71093 Genomic DNA Translation: AAC60365.1 U13983 Genomic DNA Translation: AAA62611.1 |
PIRi | I50115 |
RefSeqi | NP_571464.1, NM_131389.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
3JBW | electron microscopy | 4.63 | A/C | 271-1031 | [»] | |
3JBX | electron microscopy | 3.40 | A/C | 271-1031 | [»] | |
3JBY | electron microscopy | 3.70 | A/C | 271-1031 | [»] | |
6DBI | electron microscopy | 3.36 | A/C | 271-1031 | [»] | |
6DBJ | electron microscopy | 2.99 | A/C | 271-1031 | [»] | |
6DBL | electron microscopy | 5.00 | A/C | 271-1031 | [»] | |
6DBO | electron microscopy | 4.45 | A/C | 271-1031 | [»] | |
6DBQ | electron microscopy | 4.22 | A/C | 271-1031 | [»] | |
6DBR | electron microscopy | 4.00 | A/C | 271-1031 | [»] | |
6DBT | electron microscopy | 4.30 | A/C | 271-1031 | [»] | |
6DBU | electron microscopy | 3.90 | A/C | 271-1031 | [»] | |
6DBV | electron microscopy | 4.29 | A/C | 271-1031 | [»] | |
6DBW | electron microscopy | 4.70 | A/C | 271-1031 | [»] | |
6DBX | electron microscopy | 4.20 | A/C | 271-1031 | [»] | |
SMRi | O13033 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
STRINGi | 7955.ENSDARP00000120100 |
Proteomic databases
PaxDbi | O13033 |
Genome annotation databases
GeneIDi | 30663 |
KEGGi | dre:30663 |
Organism-specific databases
CTDi | 5896 |
ZFINi | ZDB-GENE-990415-234, rag1 |
Phylogenomic databases
eggNOGi | ENOG502QSFV, Eukaryota |
InParanoidi | O13033 |
OrthoDBi | 85196at2759 |
PhylomeDBi | O13033 |
Miscellaneous databases
PROi | PR:O13033 |
Family and domain databases
Gene3Di | 3.30.40.10, 1 hit |
InterProi | View protein in InterPro IPR024627, RAG1 IPR035714, RAG1_imp-bd IPR019485, RAG1_Znf IPR023336, RAG_nonamer-bd_dom IPR018957, Znf_C3HC4_RING-type IPR001841, Znf_RING IPR013083, Znf_RING/FYVE/PHD IPR017907, Znf_RING_CS |
PANTHERi | PTHR11539, PTHR11539, 1 hit |
Pfami | View protein in Pfam PF12940, RAG1, 1 hit PF12560, RAG1_imp_bd, 1 hit PF00097, zf-C3HC4, 1 hit |
SMARTi | View protein in SMART SM00184, RING, 1 hit |
PROSITEi | View protein in PROSITE PS51487, NBD, 1 hit PS51765, ZF_RAG1, 1 hit PS00518, ZF_RING_1, 1 hit PS50089, ZF_RING_2, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | RAG1_DANRE | |
Accessioni | O13033Primary (citable) accession number: O13033 Secondary accession number(s): Q90258 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | November 15, 2002 |
Last sequence update: | July 1, 1997 | |
Last modified: | February 23, 2022 | |
This is version 131 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families