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Entry version 99 (11 Dec 2019)
Sequence version 1 (01 Nov 1996)
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Protein

V(D)J recombination-activating protein 1

Gene

rag1

Organism
Oncorhynchus mykiss (Rainbow trout) (Salmo gairdneri)
Status
Reviewed-Annotation score:

Annotation score:4 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Protein inferred from homologyi <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>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

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi286Zinc 1By similarity1
Metal bindingi290Zinc 1By similarity1
Metal bindingi310Zinc 2By similarity1
Metal bindingi313Zinc 1By similarity1
Metal bindingi313Zinc 2By similarity1
Metal bindingi315Zinc 1By similarity1
Metal bindingi325Zinc 3By similarity1
Metal bindingi327Zinc 3By similarity1
Metal bindingi330Zinc 2By similarity1
Metal bindingi333Zinc 2By similarity1
Metal bindingi345Zinc 3By similarity1
Metal bindingi348Zinc 3By similarity1
Metal bindingi375Zinc 4By similarity1
Metal bindingi380Zinc 4By similarity1
Metal bindingi392Zinc 4By similarity1
Metal bindingi396Zinc 4By similarity1
Metal bindingi633Divalent metal cation; catalyticBy similarity1
Metal bindingi743Divalent metal cation; catalyticBy similarity1
<p>This subsection describes interesting single amino acid sites on the sequence that are not defined in any other subsection. This subsection can be displayed in different sections ('Function', 'PTM / Processing', 'Pathology and Biotech') according to its content.<p><a href='/help/site' target='_top'>More...</a></p>Sitei928Essential for DNA hairpin formation, participates in base-stacking interactions near the cleavage siteBy similarity1
Metal bindingi997Divalent metal cation; catalyticBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section specifies the position(s) and type(s) of zinc fingers within the protein.<p><a href='/help/zn_fing' target='_top'>More...</a></p>Zinc fingeri310 – 349RING-typePROSITE-ProRule annotationAdd BLAST40
Zinc fingeri371 – 400RAG1-typePROSITE-ProRule annotationAdd BLAST30
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section specifies the position and type of each DNA-binding domain present within the protein.<p><a href='/help/dna_bind' target='_top'>More...</a></p>DNA bindingi421 – 488NBDPROSITE-ProRule annotationAdd BLAST68

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionChromatin regulator, DNA-binding, Endonuclease, Hydrolase, Multifunctional enzyme, Nuclease, Transferase
Biological processDNA recombination, Ubl conjugation pathway
LigandMetal-binding, Zinc

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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:2.3.2.27)
Alternative name(s):
RING-type E3 ubiquitin transferase RAG1Curated
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:rag1
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiOncorhynchus mykiss (Rainbow trout) (Salmo gairdneri)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri8022 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiProtacanthopterygiiSalmoniformesSalmonidaeSalmoninaeOncorhynchus

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Keywords - Cellular componenti

Nucleus

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000560111 – 1073V(D)J recombination-activating protein 1Add BLAST1073

Proteomic databases

PRoteomics IDEntifications database

More...
PRIDEi
Q91187

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.

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

By similarity

GO - Molecular functioni

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
Q91187

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides general information on the biological role of a domain. The term 'domain' is intended here in its wide acceptation, it may be a structural domain, a transmembrane region or a functional domain. Several domains are described in this subsection.<p><a href='/help/domain_cc' target='_top'>More...</a></p>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

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the RAG1 family.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri310 – 349RING-typePROSITE-ProRule annotationAdd BLAST40
Zinc fingeri371 – 400RAG1-typePROSITE-ProRule annotationAdd BLAST30

Keywords - Domaini

Zinc-finger

Phylogenomic databases

Database of Orthologous Groups

More...
OrthoDBi
85196at2759

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.30.40.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR024627, RAG1
IPR035714, RAG1_imp-bd
IPR019485, RAG1_Znf
IPR023336, RAG_nonamer-bd_dom
IPR001841, Znf_RING
IPR013083, Znf_RING/FYVE/PHD
IPR017907, Znf_RING_CS

The PANTHER Classification System

More...
PANTHERi
PTHR11539, PTHR11539, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF12940, RAG1, 1 hit
PF12560, RAG1_imp_bd, 1 hit

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00184, RING, 1 hit

PROSITE; a protein domain and family database

More...
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

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

Q91187-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MEETYAPRCS MPAELHHPYS KFSDWKFKLF RVRSMERAPL PGEMQLERGA
60 70 80 90 100
LSGVVASAPL GETVGDVVGL PGSVMKLWLG GKSKENVEGP GKRVDLKLQE
110 120 130 140 150
MDTYMNHLRC LCRLCGGALR KAKGPEHEVQ GLLDEASMSA LRRVGCKATS
160 170 180 190 200
WPEVILKVFK VDVAGDMEVV HPPFFCQRCW TLAMRGGGFC SFSRTHVPGW
210 220 230 240 250
RPHTTLCLLC TPRNPHYRGE RKRRKPTRGA QHLAKRTKWD LQDNAAIVGE
260 270 280 290 300
KRAWRTVIDP PQGPGLRPWV RSSVQRAQWV KSITLCQKEH LSARLLSEDL
310 320 330 340 350
PVDFLSSVTC QVCDHLLSEP VQSPCRHLFC RSCIAKYIYS LGPHCPACTL
360 370 380 390 400
PCGPADLTAP AKGFLGVLHS LPLLCPRESC GEQVRLDSFR AHCLGHHLEE
410 420 430 440 450
VDGDHKSAEN SLDNFLPVNK GGRPRQHLLS LTRRAQKHRL RDLKTQVKVF
460 470 480 490 500
AEKEEGGDTK SVCLTLFLLA LRAGNEHRQA DELEAMMQGR GFGLHPAVCL
510 520 530 540 550
AIRVNTFLSC SQYHKMYRTV KATSGRQIFQ PLHTLRTAEK ELLPGYHPFE
560 570 580 590 600
WQPALKSVST SCHVGIIDGL SGWIASVDDS PADTVTRRFR YDVALVSALK
610 620 630 640 650
DLEEDIMEGL RERGLEDSAC TSGFSVMIKE SCDGMGDVSE KHGGGPPVPE
660 670 680 690 700
KPVRFSFTIM SVSIQAEGED EAITIFREPK PNSEMSCKPL SLMFVDESDH
710 720 730 740 750
ETLTGVLGPV VAERNAMKHS RLILSVGGLS RSFRFHFRGT GYDEKMVREM
760 770 780 790 800
EGLEASGSTY ICTLCDSTRA EASQNMTLHS VTRSHDENLE RYELWRTNPH
810 820 830 840 850
SESAEELRDR VKGVSAKPFM ETQPTLDALH CDIGNATEFY KIFQDEIGEV
860 870 880 890 900
YHKANPSREQ RRSWRAALDK QLRKKMKLKP VMRMNGNYAR KLMTREAVEA
910 920 930 940 950
VCELVCSEER QEALRELMGL YIQMKPVWRS TCPAKECPDE LCRYSFNSQR
960 970 980 990 1000
FAELLSTVFK YRYDGKITNY LHKTLAHVPE IVERDGSIGA WASEGNESGN
1010 1020 1030 1040 1050
KLFRRFRKMN ARQSKTFELE DVLKHHWLYT SKYLQKFMEA HKDSAKALQA
1060 1070
TIDTVGSQET QEDADMSLDV PDF
Length:1,073
Mass (Da):121,045
Last modified:November 1, 1996 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iC0B8308008B709B5
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U15663 Genomic DNA Translation: AAA80281.1

Protein sequence database of the Protein Information Resource

More...
PIRi
I51055

NCBI Reference Sequences

More...
RefSeqi
NP_001118209.1, NM_001124737.1

Genome annotation databases

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
100136833

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U15663 Genomic DNA Translation: AAA80281.1
PIRiI51055
RefSeqiNP_001118209.1, NM_001124737.1

3D structure databases

SMRiQ91187
ModBaseiSearch...

Proteomic databases

PRIDEiQ91187

Genome annotation databases

GeneIDi100136833

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
5896

Phylogenomic databases

OrthoDBi85196at2759

Family and domain databases

Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR024627, RAG1
IPR035714, RAG1_imp-bd
IPR019485, RAG1_Znf
IPR023336, RAG_nonamer-bd_dom
IPR001841, Znf_RING
IPR013083, Znf_RING/FYVE/PHD
IPR017907, Znf_RING_CS
PANTHERiPTHR11539, PTHR11539, 1 hit
PfamiView protein in Pfam
PF12940, RAG1, 1 hit
PF12560, RAG1_imp_bd, 1 hit
SMARTiView protein in SMART
SM00184, RING, 1 hit
PROSITEiView protein in PROSITE
PS51487, NBD, 1 hit
PS51765, ZF_RAG1, 1 hit
PS00518, ZF_RING_1, 1 hit
PS50089, ZF_RING_2, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRAG1_ONCMY
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q91187
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: December 11, 2019
This is version 99 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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