Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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 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 (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 bindingi270 – 2701Zinc 1By similarity
Metal bindingi274 – 2741Zinc 1By similarity
Metal bindingi294 – 2941Zinc 2By similarity
Metal bindingi297 – 2971Zinc 1By similarity
Metal bindingi297 – 2971Zinc 2By similarity
Metal bindingi299 – 2991Zinc 1By similarity
Metal bindingi309 – 3091Zinc 3By similarity
Metal bindingi311 – 3111Zinc 3By similarity
Metal bindingi314 – 3141Zinc 2By similarity
Metal bindingi317 – 3171Zinc 2By similarity
Metal bindingi329 – 3291Zinc 3By similarity
Metal bindingi332 – 3321Zinc 3By similarity
Metal bindingi359 – 3591Zinc 4By similarity
Metal bindingi364 – 3641Zinc 4By similarity
Metal bindingi376 – 3761Zinc 4By similarity
Metal bindingi380 – 3801Zinc 4By similarity
Metal bindingi606 – 6061Divalent metal cation; catalyticBy similarity
Metal bindingi714 – 7141Divalent metal cation; catalyticBy similarity
Sitei899 – 8991Essential for DNA hairpin formation, participates in base-stacking interactions near the cleavage siteBy similarity
Metal bindingi968 – 9681Divalent metal cation; catalyticBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri294 – 33340RING-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri355 – 38430RAG1-typePROSITE-ProRule annotationAdd
BLAST
DNA bindingi395 – 46268NBDPROSITE-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
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)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10451045V(D)J recombination-activating protein 1PRO_0000056012Add
BLAST

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.
SMRiQ91829. Positions 269-384.
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 fingeri294 – 33340RING-typePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri355 – 38430RAG1-typePROSITE-ProRule annotationAdd
BLAST

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.
SMRiQ91829. Positions 269-384.
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: July 6, 2016
This is version 89 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.