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Protein

V(D)J recombination-activating protein 1

Gene

RAG1

Organism
Sus scrofa (Pig)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

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. The chromatin structure plays an essential role in the V(D)J recombination reactions and the presence of histone H3 trimethylated at 'Lys-4' (H3K4me3) stimulates both the nicking and haipinning steps. The RAG complex also plays a role in pre-B cell allelic exclusion, a process leading to expression of a single immunoglobulin heavy chain allele to enforce clonality and monospecific recognition by the B-cell antigen receptor (BCR) expressed on individual B-lymphocytes. The introduction of DNA breaks by the RAG complex on one immunoglobulin allele induces ATM-dependent repositioning of the other allele to pericentromeric heterochromatin, preventing accessibility to the RAG complex and recombination of the second allele. In addition to its endonuclease activity, RAG1 also acts as a E3 ubiquitin-protein ligase that mediates monoubiquitination of histone H3. Histone H3 monoubiquitination is required for the joining step of V(D)J recombination. Mediates polyubiquitination of KPNA1 (By similarity).By similarity

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Binds 1 divalent metal cation per subunit. Mg2+ or Mn2+.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi269 – 2691Zinc 1By similarity
Metal bindingi273 – 2731Zinc 1By similarity
Metal bindingi293 – 2931Zinc 2By similarity
Metal bindingi296 – 2961Zinc 1By similarity
Metal bindingi296 – 2961Zinc 2By similarity
Metal bindingi298 – 2981Zinc 1By similarity
Metal bindingi308 – 3081Zinc 3By similarity
Metal bindingi310 – 3101Zinc 3By similarity
Metal bindingi313 – 3131Zinc 2By similarity
Metal bindingi316 – 3161Zinc 2By similarity
Metal bindingi328 – 3281Zinc 3By similarity
Metal bindingi331 – 3311Zinc 3By similarity
Metal bindingi358 – 3581Zinc 4By similarity
Metal bindingi363 – 3631Zinc 4By similarity
Metal bindingi375 – 3751Zinc 4By similarity
Metal bindingi379 – 3791Zinc 4By similarity
Metal bindingi603 – 6031Divalent metal cation; catalyticBy similarity
Metal bindingi711 – 7111Divalent metal cation; catalyticBy similarity
Sitei896 – 8961Essential for DNA hairpin formation, participates in base-stacking interactions near the cleavage siteBy similarity
Metal bindingi965 – 9651Divalent metal cation; catalyticBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri293 – 33240RING-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri354 – 38330RAG1-typePROSITE-ProRule annotationAdd
BLAST
DNA bindingi392 – 45968NBDPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Endonuclease, Hydrolase, Ligase, Nuclease

Keywords - Biological processi

DNA recombination, Ubl conjugation pathway

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
V(D)J recombination-activating protein 1
Short name:
RAG-1
Including the following 2 domains:
Endonuclease RAG1 (EC:3.1.-.-)
E3 ubiquitin-protein ligase RAG1 (EC:6.3.2.-)
Gene namesi
Name:RAG1
OrganismiSus scrofa (Pig)
Taxonomic identifieri9823 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaSuinaSuidaeSus
Proteomesi
  • UP000008227 Componenti: Unplaced

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10431043V(D)J recombination-activating protein 1PRO_0000056006Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki234 – 234Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity

Post-translational modificationi

Autoubiquitinated in the presence of CDC34/UBCH3.By similarity

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PaxDbiQ867B5.

Interactioni

Subunit structurei

Homodimer. Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2. Interacts with VPRBP, leading to recruitment of the CUL4A-RBX1-DDB1-DCAF1/VPRBP complex to ubiquitinate proteins and limit error-prone repair during V(D)J recombination (By similarity).By similarity

GO - Molecular functioni

Protein-protein interaction databases

STRINGi9823.ENSSSCP00000029411.

Structurei

3D structure databases

ProteinModelPortaliQ867B5.
SMRiQ867B5. Positions 268-383.
ModBaseiSearch...
MobiDBiSearch...

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
Contains 1 NBD (nonamer binding) DNA-binding domain.PROSITE-ProRule annotation
Contains 1 RAG1-type zinc finger.PROSITE-ProRule annotationCurated
Contains 1 RING-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri293 – 33240RING-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri354 – 38330RAG1-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiENOG410IKNG. Eukaryota.
ENOG4110KH0. LUCA.
HOVERGENiHBG003861.
InParanoidiQ867B5.
KOiK10628.

Family and domain databases

Gene3Di3.30.160.60. 1 hit.
3.30.40.10. 1 hit.
InterProiIPR024627. RAG1.
IPR019485. RAG1_Znf.
IPR023336. RAG_nonamer-bd_dom.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PANTHERiPTHR11539. PTHR11539. 1 hit.
PfamiPF12940. RAG1. 1 hit.
PF10426. zf-RAG1. 1 hit.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS51487. NBD. 1 hit.
PS51765. ZF_RAG1. 1 hit.
PS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q867B5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAVSLPPTLG LSSAPDEIQH PHIKFSEWKF KLFRVRSFEK APEKAQTEKQ
60 70 80 90 100
DSSEGKPSLE QSPAVLDKPG GQKSALPQPA FKPHPKFLKE SHEDGKARDK
110 120 130 140 150
AIHQANLRRL CRICGNSFNT TGHKRRYPVH GPVDGKTQVL LRKKEKRATS
160 170 180 190 200
WPDLIAKVFR IDVKADVDSI HPTEFCHNCW SFMHRKFSST PCEVYSPRNA
210 220 230 240 250
AMEWHPHTLN CDICHIARRG LKRKSQQPNM QLSKKLKTVI DRARQARQRK
260 270 280 290 300
RRAQARISSK ELMKKIANCG QIHLSPKLLA VDFPAHFVKS ISCQICEHIL
310 320 330 340 350
ADPVETSCKH VFCRICILRC LKVMGSSCPS CHYPCFPTDL ESPVKSFLSI
360 370 380 390 400
LNTLMVKCPA KECNEEISLE KYNHHISSHK ESKETFVHIN KGGRPRQHLL
410 420 430 440 450
SLTRRAQKHR LRELKLQVKA FADKEEGGDV KSVCLTLFLL VLRARNEHRQ
460 470 480 490 500
ADELEAIMRG QGSGLQPAVC LAIRVNTFLS CSQYHKMYRT VKAITGRQIF
510 520 530 540 550
QPLHALRNAE KVLLPGYHPF EWQPPLKNVS SSTDVGIIDG LSGLSSSVDD
560 570 580 590 600
YPVDTIAKRF RYDSALVSAL MDMEEDILEG MRAQDLDDYL NGPFTVVVKE
610 620 630 640 650
SCDGMGDVSE KHGSGPVVPE KAVRFSFTVM KITIAHGSQN VKVFEEAKPN
660 670 680 690 700
SELCCKPLCL MLADESDHET LTAILSPLIA EREAMKSSQL MLEMGGILRT
710 720 730 740 750
FKFIFRGTGY DEKLVREVEG LEASGSVYIC TLCDATRLEA SQNLVFHSIT
760 770 780 790 800
RSHAENLERY EVWRSNPYHE TVDELRDRVK GVSAKPFIET VPSIDALHCD
810 820 830 840 850
IGNAAEFYKI FQLEIGEAYK NPHASKEERK RWQATLDKHL RKKMNLKPIM
860 870 880 890 900
RMNGNFARKL MTKETVEAVC ELIPSEERHE ALRELMDLYL KMKPVWRSSC
910 920 930 940 950
PAKECPESLC QYSFNSQRFA ELLSTKFKYR YEGKITNYFH KTLAHVPEII
960 970 980 990 1000
ERDGSIGAWA SEGNESGNKL FRRFRKMNAR QSKYYEMEDV LKHHWLYTSK
1010 1020 1030 1040
YLQKFMNAHK AFKNSGFTIN LQRSSGDTLD LENSPESQDL MEF
Length:1,043
Mass (Da):119,068
Last modified:June 1, 2003 - v1
Checksum:iD0E75CD5488690AC
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB091392 Genomic DNA. Translation: BAC54968.1.
RefSeqiNP_001116656.1. NM_001123184.1.
UniGeneiSsc.16265.

Genome annotation databases

GeneIDi397506.
KEGGissc:397506.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB091392 Genomic DNA. Translation: BAC54968.1.
RefSeqiNP_001116656.1. NM_001123184.1.
UniGeneiSsc.16265.

3D structure databases

ProteinModelPortaliQ867B5.
SMRiQ867B5. Positions 268-383.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9823.ENSSSCP00000029411.

Proteomic databases

PaxDbiQ867B5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi397506.
KEGGissc:397506.

Organism-specific databases

CTDi5896.

Phylogenomic databases

eggNOGiENOG410IKNG. Eukaryota.
ENOG4110KH0. LUCA.
HOVERGENiHBG003861.
InParanoidiQ867B5.
KOiK10628.

Family and domain databases

Gene3Di3.30.160.60. 1 hit.
3.30.40.10. 1 hit.
InterProiIPR024627. RAG1.
IPR019485. RAG1_Znf.
IPR023336. RAG_nonamer-bd_dom.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PANTHERiPTHR11539. PTHR11539. 1 hit.
PfamiPF12940. RAG1. 1 hit.
PF10426. zf-RAG1. 1 hit.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS51487. NBD. 1 hit.
PS51765. ZF_RAG1. 1 hit.
PS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Porcine RAG-1 gene promoter and coding region."
    Hatsuse H., Homma D., Hiraiwa H., Yasue H., Takagaki Y.
    Submitted (SEP-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: Large white.
    Tissue: Liver.

Entry informationi

Entry nameiRAG1_PIG
AccessioniPrimary (citable) accession number: Q867B5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 24, 2006
Last sequence update: June 1, 2003
Last modified: July 6, 2016
This is version 82 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.