UniProtKB - P24271 (RAG1_CHICK)
Protein
V(D)J recombination-activating protein 1
Gene
RAG1
Organism
Gallus gallus (Chicken)
Status
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 similarity
Catalytic 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
Mg2+By similarity, Mn2+By similarityNote: Binds 1 divalent metal cation per subunit. Mg2+ or Mn2+.By similarity
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 265 | Zinc 1By similarity | 1 | |
Metal bindingi | 269 | Zinc 1By similarity | 1 | |
Metal bindingi | 289 | Zinc 2By similarity | 1 | |
Metal bindingi | 292 | Zinc 1By similarity | 1 | |
Metal bindingi | 292 | Zinc 2By similarity | 1 | |
Metal bindingi | 294 | Zinc 1By similarity | 1 | |
Metal bindingi | 304 | Zinc 3By similarity | 1 | |
Metal bindingi | 306 | Zinc 3By similarity | 1 | |
Metal bindingi | 309 | Zinc 2By similarity | 1 | |
Metal bindingi | 312 | Zinc 2By similarity | 1 | |
Metal bindingi | 324 | Zinc 3By similarity | 1 | |
Metal bindingi | 327 | Zinc 3By similarity | 1 | |
Metal bindingi | 354 | Zinc 4By similarity | 1 | |
Metal bindingi | 359 | Zinc 4By similarity | 1 | |
Metal bindingi | 371 | Zinc 4By similarity | 1 | |
Metal bindingi | 375 | Zinc 4By similarity | 1 | |
Metal bindingi | 601 | Divalent metal cation; catalyticBy similarity | 1 | |
Metal bindingi | 709 | Divalent metal cation; catalyticBy similarity | 1 | |
Sitei | 894 | Essential for DNA hairpin formation, participates in base-stacking interactions near the cleavage siteBy similarity | 1 | |
Metal bindingi | 963 | Divalent metal cation; catalyticBy similarity | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 289 – 328 | RING-typePROSITE-ProRule annotationAdd BLAST | 40 | |
Zinc fingeri | 350 – 379 | RAG1-typePROSITE-ProRule annotationAdd BLAST | 30 | |
DNA bindingi | 390 – 457 | NBDPROSITE-ProRule annotationAdd BLAST | 68 |
GO - Molecular functioni
- endonuclease activity Source: UniProtKB
- histone binding Source: UniProtKB
- metal ion binding Source: UniProtKB
- protein homodimerization activity Source: UniProtKB
- sequence-specific DNA binding Source: UniProtKB
- ubiquitin protein ligase activity Source: InterPro
- ubiquitin-protein transferase activity Source: UniProtKB
- zinc ion binding Source: UniProtKB
GO - Biological processi
- B cell differentiation Source: UniProtKB
- histone monoubiquitination Source: UniProtKB
- T cell differentiation in thymus Source: UniProtKB
- V(D)J recombination Source: UniProtKB
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 | Gallus gallus (Chicken) |
Taxonomic identifieri | 9031 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Archelosauria › Archosauria › Dinosauria › Saurischia › Theropoda › Coelurosauria › Aves › Neognathae › Galloanserae › Galliformes › Phasianidae › Phasianinae › Gallus |
Proteomesi |
|
Subcellular locationi
Nucleus
- Nucleus PROSITE-ProRule annotation
Nucleus
- nucleus Source: UniProtKB
Keywords - Cellular componenti
NucleusPTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000056008 | 1 – 1041 | V(D)J recombination-activating protein 1Add BLAST | 1041 |
Proteomic databases
PaxDbi | P24271 |
PRIDEi | P24271 |
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
Family & Domainsi
Domaini
The RING-type zinc finger mediates the E3 ubiquitin-protein ligase activity.By similarity
The NBD (nonamer binding) DNA-binding domain mediates the specific binding to the nonamer RSS motif by forming a tightly interwoven homodimer that binds and synapses 2 nonamer elements, with each NBD making contact with both DNA molecules. Each RSS is composed of well-conserved heptamer (consensus 5'-CACAGTG-3') and nonamer (consensus 5'-ACAAAAACC-3') sequences separated by a spacer of either 12 bp or 23 bp.PROSITE-ProRule annotation
Sequence similaritiesi
Belongs to the RAG1 family.PROSITE-ProRule annotation
Zinc finger
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Zinc fingeri | 289 – 328 | RING-typePROSITE-ProRule annotationAdd BLAST | 40 | |
Zinc fingeri | 350 – 379 | RAG1-typePROSITE-ProRule annotationAdd BLAST | 30 |
Keywords - Domaini
Zinc-fingerPhylogenomic databases
InParanoidi | P24271 |
OrthoDBi | 85196at2759 |
PhylomeDBi | P24271 |
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 IPR036236, Znf_C2H2_sf 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 PF10426, zf-RAG1, 1 hit |
SUPFAMi | SSF57667, SSF57667, 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 |
i Sequence
Sequence statusi: Complete.
P24271-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MSITSRMDLP EEIQHPYAKF SEWKFKLFKV RPFQKEPSDK SQCINKDQEQ
60 70 80 90 100
EVASTDKNIT LHKDEEVPRG EKLILTQKDF MGNTQALEKD VNDMKIQDNT
110 120 130 140 150
AHQNNLKQLC RICGVSFKTD CYKRTHPVHG PVDDETLWLL RKKEKKATSW
160 170 180 190 200
PDLIAKVFKI DVRGDVDTIH PTRFCHNCWS IIHRKFSNTP CEVYFPRNST
210 220 230 240 250
MEWQPHSANC EVCHTPSRGV KRKSQPPNVQ HGKRVKIIAE RARVNRGIKN
260 270 280 290 300
QVIKNKNVMK EITNCKNRHL STKLLAVDYP ADFIKSISCQ ICEHILADPV
310 320 330 340 350
ETTCRHLFCR TCILSCIRVM GCYCPSCWYP CFPTDLVTPV KSFLNILDSL
360 370 380 390 400
SIRCPVPECD EEILHGKYGQ HFSNHKEMKD KELYNPINKG GRPRQHLLSL
410 420 430 440 450
TRRAQKHRLR ELKRQVKAFA EKEEGGDIKA VCMTLFLLAL RAKNEHKQAD
460 470 480 490 500
ELEAIMQGRG SGLHPAVCLA IRINTFLSCS QYHKMYRTVK AVTGRQIFQP
510 520 530 540 550
LHALRTAEKA LLPGYHPFEW KPPLKNVSTN TEVGIIDGLS GLPLSIDDYP
560 570 580 590 600
IDTIAKRFRY DTALVSALKD MEEEILEGMK AKNLDDYLNG PFTVVVKECC
610 620 630 640 650
DGMGDVSEKH GSGPAVPEKA VRFSFTVMNI AIDHENERIR IFEEVKPNSE
660 670 680 690 700
LCCKPLCLML ADESDHETLT AILSPLIAER EAMKNSELLL EIGGILRTFK
710 720 730 740 750
FIFRGTGYDE KLVREVEGLE ASGSTYICTL CDATRLEASQ NLVFHSITRS
760 770 780 790 800
HAENLERYEI WRSNPYHESV DELRDRVKGV SAKPFIETVP SIDALHCDIG
810 820 830 840 850
NATEFYRIFQ MEIGEVYKNP DATKEERKRW QLTLDKHLRK KMKLKPMMRM
860 870 880 890 900
SGNFARKLMS KETVEAVCEL IKCEERHEAL KELMDLYLKM KPVWRSSCPA
910 920 930 940 950
KECPELLCQY SYNSQRFAEL LSTKFKYRYE GKITNYFHKT LAHVPEIIER
960 970 980 990 1000
DGSIGAWASE GNESGNKLFR RFRKMNARQS KFYEMEDVLK HHWLYTSKYL
1010 1020 1030 1040
QKFMNAHKTL RSQGFAIDPD DGLGDSLPPE ISLESNDSVE L
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | M58530 Genomic DNA Translation: AAA49051.1 |
PIRi | S42509 |
RefSeqi | NP_001026359.1, NM_001031188.1 |
Genome annotation databases
GeneIDi | 423164 |
KEGGi | gga:423164 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | M58530 Genomic DNA Translation: AAA49051.1 |
PIRi | S42509 |
RefSeqi | NP_001026359.1, NM_001031188.1 |
3D structure databases
SMRi | P24271 |
ModBasei | Search... |
Proteomic databases
PaxDbi | P24271 |
PRIDEi | P24271 |
Genome annotation databases
GeneIDi | 423164 |
KEGGi | gga:423164 |
Organism-specific databases
CTDi | 5896 |
Phylogenomic databases
InParanoidi | P24271 |
OrthoDBi | 85196at2759 |
PhylomeDBi | P24271 |
Miscellaneous databases
PROi | PR:P24271 |
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 IPR036236, Znf_C2H2_sf 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 PF10426, zf-RAG1, 1 hit |
SUPFAMi | SSF57667, SSF57667, 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 |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | RAG1_CHICK | |
Accessioni | P24271Primary (citable) accession number: P24271 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | March 1, 1992 |
Last sequence update: | March 1, 1992 | |
Last modified: | December 2, 2020 | |
This is version 130 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
Reference proteomeDocuments
- SIMILARITY comments
Index of protein domains and families