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Protein

V(D)J recombination-activating protein 1

Gene

rag1

Organism
Xenopus laevis (African clawed frog)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

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

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi270Zinc 1By similarity1
Metal bindingi274Zinc 1By similarity1
Metal bindingi294Zinc 2By similarity1
Metal bindingi297Zinc 1By similarity1
Metal bindingi297Zinc 2By similarity1
Metal bindingi299Zinc 1By similarity1
Metal bindingi309Zinc 3By similarity1
Metal bindingi311Zinc 3By similarity1
Metal bindingi314Zinc 2By similarity1
Metal bindingi317Zinc 2By similarity1
Metal bindingi329Zinc 3By similarity1
Metal bindingi332Zinc 3By similarity1
Metal bindingi359Zinc 4By similarity1
Metal bindingi364Zinc 4By similarity1
Metal bindingi376Zinc 4By similarity1
Metal bindingi380Zinc 4By similarity1
Metal bindingi606Divalent metal cation; catalyticBy similarity1
Metal bindingi714Divalent metal cation; catalyticBy similarity1
Sitei899Essential for DNA hairpin formation, participates in base-stacking interactions near the cleavage siteBy similarity1
Metal bindingi968Divalent metal cation; catalyticBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri294 – 333RING-typePROSITE-ProRule annotationAdd BLAST40
Zinc fingeri355 – 384RAG1-typePROSITE-ProRule annotationAdd BLAST30
DNA bindingi395 – 462NBDPROSITE-ProRule annotationAdd BLAST68

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
OrganismiXenopus laevis (African clawed frog)
Taxonomic identifieri8355 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusXenopus

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000560121 – 1045V(D)J recombination-activating protein 1Add BLAST1045

Expressioni

Tissue specificityi

Expressed within the thymus, liver and spleen in juvenile frogs, and within the thymus and bone marrow of adults.

Interactioni

Subunit structurei

Homodimer. Component of the RAG complex composed of core components rag1 and rag2 (By similarity).By similarity

GO - Molecular functioni

Structurei

3D structure databases

ProteinModelPortaliQ91829.
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)DescriptionActionsGraphical viewLength
Zinc fingeri294 – 333RING-typePROSITE-ProRule annotationAdd BLAST40
Zinc fingeri355 – 384RAG1-typePROSITE-ProRule annotationAdd BLAST30

Keywords - Domaini

Zinc-finger

Phylogenomic databases

HOVERGENiHBG003861.
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.
IPR018957. Znf_C3HC4_RING-type.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PANTHERiPTHR11539. PTHR11539. 1 hit.
PfamiPF12940. RAG1. 1 hit.
PF00097. zf-C3HC4. 1 hit.
PF10426. zf-RAG1. 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.

Q91829-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEVALPNVPT KMQHPFTKYS EWKFKLFRVK SLERRPSEEE TEGSEVSYNS
60 70 80 90 100
SQETYPKSTV VLEDLSLGSA PQSPTNFKPQ QSEKSNVVDN HETDLKRLEE
110 120 130 140 150
EAHITVIQQL CRICGASFKM DQQNRSYPVH GPVDSETHDI LRRREKKVTS
160 170 180 190 200
WPELISKVFK TDVRADVDTI HPTQFCHNCW TIMNQKFSNI SSEVYFPHNQ
210 220 230 240 250
AVEWTPHSAN CYVCHSSKPW GKRKSAPQLN PHKMKKRKRG PEFVKKSKTS
260 270 280 290 300
SGNSIQWKNM KAFNQMKDSC KKIHLDNNLL VLDYPSDFVK SVSCLVCEHI
310 320 330 340 350
LSDPVQTSCK HLFCRICILK YIKLMGCYCP SCKYPCFPTD LTVPVKSYLN
360 370 380 390 400
VLNALLLKCT VSGCDEEISL GKYSHHISKH KETKGKEVYA HINKGGRPRQ
410 420 430 440 450
HLLTLTRRAQ KHRLRELKMQ VKAFADKEEE GDVKSVCLTL FLLALRARNE
460 470 480 490 500
HRQADELEAI MEGRGAGLHP AVCLAIRVNT FLSCSQYHKM YRTVKATTGR
510 520 530 540 550
QIFQPLHALR NAEKALIPGY HTFEWRPPLK NVSTRTDVGI IDGLSGLNQS
560 570 580 590 600
LDEYPVDTIS KRFRYDAALV SALKDMEEDI LEGLKAQDLD DYVSGPFTVV
610 620 630 640 650
VKESCDGMGD VSEKHGSGPP VPEKAVRFSF TVMNISVPNK NGPVRIFEET
660 670 680 690 700
KPNSELCCKP LCLMLADESD HETLTAILSP LIAEREAMKT AELLLEMGGI
710 720 730 740 750
LRNFKFSFRG TGYDEKLVRE VEGLEASGSL YICTLCDATR LEAAQNLVNH
760 770 780 790 800
SITRSHCENL QRYEMWRSNP HHESPDELRD RVKGVSAKPF IETLPSIDAL
810 820 830 840 850
HCDIGNAAEF YRIFQLEIGE LYKNLSATKE EKKRWQATLD NHIRKRMNLK
860 870 880 890 900
PIMRMNGNFA RKLMSKETVE AVCELVPCEE RQAALTELMD LYLKMKPVWR
910 920 930 940 950
SSCPAKECPE LLCQYSFHSQ RFAELLSTKF KYRYEGKITN YFHKTLAHVP
960 970 980 990 1000
EIIERDGSIG AWASEGNESG NKLFRRFRKM NARQSKFYEM EDVLKHHWLY
1010 1020 1030 1040
TSKYLQKFMN AHNNLKNQGF TVDLDNPDLE QRLESSMESL ESMEF
Length:1,045
Mass (Da):119,893
Last modified:November 1, 1996 - v1
Checksum:i93F45B5E77590153
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L19324 Genomic DNA. Translation: AAA03068.1.
PIRiI51555.
RefSeqiNP_001165554.1. NM_001172083.1.
UniGeneiXl.85728.

Genome annotation databases

GeneIDi100337558.
KEGGixla:100337558.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L19324 Genomic DNA. Translation: AAA03068.1.
PIRiI51555.
RefSeqiNP_001165554.1. NM_001172083.1.
UniGeneiXl.85728.

3D structure databases

ProteinModelPortaliQ91829.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100337558.
KEGGixla:100337558.

Organism-specific databases

CTDi5896.

Phylogenomic databases

HOVERGENiHBG003861.
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.
IPR018957. Znf_C3HC4_RING-type.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PANTHERiPTHR11539. PTHR11539. 1 hit.
PfamiPF12940. RAG1. 1 hit.
PF00097. zf-C3HC4. 1 hit.
PF10426. zf-RAG1. 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...

Entry informationi

Entry nameiRAG1_XENLA
AccessioniPrimary (citable) accession number: Q91829
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: November 30, 2016
This is version 91 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

Multifunctional enzyme

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.