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P21784

- RAG2_MOUSE

UniProt

P21784 - RAG2_MOUSE

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Protein

V(D)J recombination-activating protein 2

Gene

Rag2

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Core 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. DNA cleavage by the RAG complex 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 the RAG complex, RAG2 is not the catalytic component but is required for all known catalytic activities mediated by RAG1. It probably acts as a sensor of chromatin state that recruits the RAG complex to H3K4me3.6 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi419 – 4191Zinc 12 Publications
Metal bindingi423 – 4231Zinc 12 Publications
Metal bindingi446 – 4461Zinc 22 Publications
Metal bindingi452 – 4521Zinc 22 Publications
Metal bindingi455 – 4551Zinc 12 Publications
Metal bindingi458 – 4581Zinc 12 Publications
Metal bindingi478 – 4781Zinc 22 Publications
Metal bindingi481 – 4811Zinc 22 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri416 – 48469PHD-type; atypicalAdd
BLAST

GO - Molecular functioni

  1. chromatin binding Source: UniProtKB
  2. DNA binding Source: InterPro
  3. methylated histone binding Source: UniProtKB
  4. phosphatidylinositol-3,4,5-trisphosphate binding Source: UniProtKB
  5. phosphatidylinositol-3,4-bisphosphate binding Source: UniProtKB
  6. phosphatidylinositol-3,5-bisphosphate binding Source: UniProtKB
  7. phosphatidylinositol-4,5-bisphosphate binding Source: UniProtKB
  8. phosphatidylinositol binding Source: UniProtKB
  9. zinc ion binding Source: UniProtKB

GO - Biological processi

  1. B cell differentiation Source: UniProtKB
  2. B cell homeostatic proliferation Source: MGI
  3. B cell lineage commitment Source: MGI
  4. chromatin modification Source: UniProtKB-KW
  5. DNA recombination Source: MGI
  6. positive regulation of organ growth Source: MGI
  7. pre-B cell allelic exclusion Source: UniProtKB
  8. T cell differentiation Source: MGI
  9. T cell differentiation in thymus Source: UniProtKB
  10. T cell lineage commitment Source: MGI
  11. V(D)J recombination Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator

Keywords - Biological processi

DNA recombination

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
V(D)J recombination-activating protein 2
Short name:
RAG-2
Gene namesi
Name:Rag2
Synonyms:Rag-2
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 2

Organism-specific databases

MGIiMGI:97849. Rag2.

Subcellular locationi

GO - Cellular componenti

  1. nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Mice are viable but fail to produce mature B or T-lymphocytes. Very immature lymphoid cells are present in primary lymphoid organs. These cells do not rearrange their immunoglobulin or T-cell receptor loci. Double knockout with TREX1 does not show a visible phenotype.2 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi128 – 1281D → N: Does not affect the endonuclease activity of the RAG complex. 1 Publication
Mutagenesisi199 – 1991E → Q: Does not affect the endonuclease activity of the RAG complex. 1 Publication
Mutagenesisi202 – 2021D → N: Does not affect the endonuclease activity of the RAG complex. 1 Publication
Mutagenesisi280 – 2801E → Q: Does not affect the endonuclease activity of the RAG complex. 1 Publication
Mutagenesisi310 – 3101D → N: Does not affect the endonuclease activity of the RAG complex. 1 Publication
Mutagenesisi358 – 3581D → N: Does not affect the endonuclease activity of the RAG complex. 1 Publication
Mutagenesisi374 – 3741D → N: Does not affect the endonuclease activity of the RAG complex. 1 Publication
Mutagenesisi402 – 4021Y → A: Reduced interaction with histones. 1 Publication
Mutagenesisi403 – 4031N → A: Reduced interaction with histones. 1 Publication
Mutagenesisi406 – 4061D → A: Reduced interaction with histones. 1 Publication
Mutagenesisi407 – 4071E → A: Reduced interaction with histones. 1 Publication
Mutagenesisi408 – 4081D → A: Induces a slight reduction in V(D)J recombination without affecting interaction with histones.
Mutagenesisi415 – 4151Y → A: Abolishes binding to H3K4me3 without affecting phosphoinositide-binding. 1 Publication
Mutagenesisi440 – 4401K → A: Binds PtdIns(4,5)P2 at wild-type level. 1 Publication
Mutagenesisi443 – 4431M → A: Abolishes binding to H3K4me3 without affecting phosphoinositide-binding. 1 Publication
Mutagenesisi445 – 4451Y → A or D: Still binds H3K4me3 and H3R2me2 but with reduced affinity. 1 Publication
Mutagenesisi453 – 4531W → R: Abolishes binding to H3K4me3 without affecting phosphoinositide-binding. Impairs enzymatic activity of the RAG complex. 2 Publications
Mutagenesisi464 – 4641R → A: Leads to a strong reduction in PtdIns(4,5)P2-binding. 1 Publication
Mutagenesisi468 – 4681H → A: Leads to a strong reduction in PtdIns(4,5)P2-binding. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 527527V(D)J recombination-activating protein 2PRO_0000167138Add
BLAST

Proteomic databases

PRIDEiP21784.

PTM databases

PhosphoSiteiP21784.

Expressioni

Tissue specificityi

Maturing lymphoid cells.

Gene expression databases

BgeeiP21784.
CleanExiMM_RAG2.
ExpressionAtlasiP21784. baseline.
GenevestigatoriP21784.

Interactioni

Subunit structurei

Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2.4 Publications

Protein-protein interaction databases

BioGridi202575. 1 interaction.
DIPiDIP-46179N.
IntActiP21784. 3 interactions.
MINTiMINT-8384500.

Structurei

Secondary structure

1
527
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi414 – 4174
Turni427 – 4293
Beta strandi434 – 4363
Beta strandi438 – 4403
Beta strandi443 – 4464
Beta strandi448 – 4503
Beta strandi452 – 4554
Helixi457 – 4593
Helixi463 – 4719
Turni479 – 4835

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2JWONMR-A414-487[»]
2V83X-ray2.40A/B/C414-487[»]
2V85X-ray2.00A/B414-487[»]
2V86X-ray2.05A/B414-487[»]
2V87X-ray1.80A/B414-487[»]
2V88X-ray2.00A/B414-487[»]
2V89X-ray1.10A/B414-487[»]
ProteinModelPortaliP21784.
SMRiP21784. Positions 414-487.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP21784.

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi352 – 41059Asp/Glu-rich (acidic)Add
BLAST

Domaini

The atypical PHD-type zinc finger recognizes and binds histone H3 trimethylated on 'Lys-4' (H3K4me3). The presence Tyr-445 instead of a carboxylate in classical PHD-type zinc fingers results in an enhanced binding to H3K4me3 in presence of dimethylated on 'Arg-2' (H3R2me2) rather than inhibited. The atypical PHD-type zinc finger also binds various phosphoinositides, such as phosphatidylinositol 3,4-bisphosphate binding (PtdIns(3,4)P2), phosphatidylinositol 3,5-bisphosphate binding (PtdIns(3,5)P2), phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2) and phosphatidylinositol 3,4,5-trisphosphate binding (PtdIns(3,4,5)P3).2 Publications

Sequence similaritiesi

Belongs to the RAG2 family.Curated
Contains 1 PHD-type zinc finger.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri416 – 48469PHD-type; atypicalAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG39310.
HOGENOMiHOG000237346.
HOVERGENiHBG006694.
InParanoidiP21784.
KOiK10988.
OMAiFGQKGWP.
OrthoDBiEOG73804B.
PhylomeDBiP21784.
TreeFamiTF331236.

Family and domain databases

Gene3Di2.120.10.80. 1 hit.
InterProiIPR011043. Gal_Oxase/kelch_b-propeller.
IPR015915. Kelch-typ_b-propeller.
IPR004321. RAG2.
IPR025162. RAG2_PHD.
IPR011011. Znf_FYVE_PHD.
[Graphical view]
PANTHERiPTHR10960. PTHR10960. 1 hit.
PfamiPF03089. RAG2. 1 hit.
PF13341. RAG2_PHD. 1 hit.
[Graphical view]
SUPFAMiSSF50965. SSF50965. 1 hit.
SSF57903. SSF57903. 1 hit.

Sequencei

Sequence statusi: Complete.

P21784-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSLQMVTVGH NIALIQPGFS LMNFDGQVFF FGQKGWPKRS CPTGVFHFDI
60 70 80 90 100
KQNHLKLKPA IFSKDSCYLP PLRYPATCSY KGSIDSDKHQ YIIHGGKTPN
110 120 130 140 150
NELSDKIYIM SVACKNNKKV TFRCTEKDLV GDVPEPRYGH SIDVVYSRGK
160 170 180 190 200
SMGVLFGGRS YMPSTQRTTE KWNSVADCLP HVFLIDFEFG CATSYILPEL
210 220 230 240 250
QDGLSFHVSI ARNDTVYILG GHSLASNIRP ANLYRIRVDL PLGTPAVNCT
260 270 280 290 300
VLPGGISVSS AILTQTNNDE FVIVGGYQLE NQKRMVCSLV SLGDNTIEIS
310 320 330 340 350
EMETPDWTSD IKHSKIWFGS NMGNGTIFLG IPGDNKQAMS EAFYFYTLRC
360 370 380 390 400
SEEDLSEDQK IVSNSQTSTE DPGDSTPFED SEEFCFSAEA TSFDGDDEFD
410 420 430 440 450
TYNEDDEDDE SVTGYWITCC PTCDVDINTW VPFYSTELNK PAMIYCSHGD
460 470 480 490 500
GHWVHAQCMD LEERTLIHLS EGSNKYYCNE HVQIARALQT PKRNPPLQKP
510 520
PMKSLHKKGS GKVLTPAKKS FLRRLFD
Length:527
Mass (Da):59,074
Last modified:July 15, 1998 - v2
Checksum:i51086F95A4A664A7
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M64796 mRNA. Translation: AAB82302.1.
CCDSiCCDS16462.1.
PIRiA34852.
RefSeqiNP_033046.1. NM_009020.3.
UniGeneiMm.4988.

Genome annotation databases

EnsembliENSMUST00000044031; ENSMUSP00000038204; ENSMUSG00000032864.
ENSMUST00000111227; ENSMUSP00000106858; ENSMUSG00000032864.
GeneIDi19374.
KEGGimmu:19374.
UCSCiuc008lhj.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
M64796 mRNA. Translation: AAB82302.1 .
CCDSi CCDS16462.1.
PIRi A34852.
RefSeqi NP_033046.1. NM_009020.3.
UniGenei Mm.4988.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2JWO NMR - A 414-487 [» ]
2V83 X-ray 2.40 A/B/C 414-487 [» ]
2V85 X-ray 2.00 A/B 414-487 [» ]
2V86 X-ray 2.05 A/B 414-487 [» ]
2V87 X-ray 1.80 A/B 414-487 [» ]
2V88 X-ray 2.00 A/B 414-487 [» ]
2V89 X-ray 1.10 A/B 414-487 [» ]
ProteinModelPortali P21784.
SMRi P21784. Positions 414-487.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 202575. 1 interaction.
DIPi DIP-46179N.
IntActi P21784. 3 interactions.
MINTi MINT-8384500.

PTM databases

PhosphoSitei P21784.

Proteomic databases

PRIDEi P21784.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000044031 ; ENSMUSP00000038204 ; ENSMUSG00000032864 .
ENSMUST00000111227 ; ENSMUSP00000106858 ; ENSMUSG00000032864 .
GeneIDi 19374.
KEGGi mmu:19374.
UCSCi uc008lhj.1. mouse.

Organism-specific databases

CTDi 5897.
MGIi MGI:97849. Rag2.

Phylogenomic databases

eggNOGi NOG39310.
HOGENOMi HOG000237346.
HOVERGENi HBG006694.
InParanoidi P21784.
KOi K10988.
OMAi FGQKGWP.
OrthoDBi EOG73804B.
PhylomeDBi P21784.
TreeFami TF331236.

Miscellaneous databases

EvolutionaryTracei P21784.
NextBioi 296467.
PROi P21784.
SOURCEi Search...

Gene expression databases

Bgeei P21784.
CleanExi MM_RAG2.
ExpressionAtlasi P21784. baseline.
Genevestigatori P21784.

Family and domain databases

Gene3Di 2.120.10.80. 1 hit.
InterProi IPR011043. Gal_Oxase/kelch_b-propeller.
IPR015915. Kelch-typ_b-propeller.
IPR004321. RAG2.
IPR025162. RAG2_PHD.
IPR011011. Znf_FYVE_PHD.
[Graphical view ]
PANTHERi PTHR10960. PTHR10960. 1 hit.
Pfami PF03089. RAG2. 1 hit.
PF13341. RAG2_PHD. 1 hit.
[Graphical view ]
SUPFAMi SSF50965. SSF50965. 1 hit.
SSF57903. SSF57903. 1 hit.
ProtoNeti Search...

Publicationsi

  1. "RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination."
    Oettinger M.A., Schatz D.G., Gorka C., Baltimore D.
    Science 248:1517-1523(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
  2. Oettinger M.A., Schatz D.G., Gorka C., Baltimore D.
    Submitted (NOV-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: SEQUENCE REVISION TO 458.
  3. "RAG-2-deficient mice lack mature lymphocytes owing to inability to initiate V(D)J rearrangement."
    Shinkai Y., Rathbun G., Lam K.P., Oltz E.M., Stewart V., Mendelsohn M., Charron J., Datta M., Young F., Stall A.M., Alt F.W.
    Cell 68:855-867(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
  4. "Cleavage at a V(D)J recombination signal requires only RAG1 and RAG2 proteins and occurs in two steps."
    McBlane J.F., van Gent D.C., Ramsden D.A., Romeo C., Cuomo C.A., Gellert M., Oettinger M.A.
    Cell 83:387-395(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH RAG1.
  5. "RAG1 and RAG2 form a stable postcleavage synaptic complex with DNA containing signal ends in V(D)J recombination."
    Agrawal A., Schatz D.G.
    Cell 89:43-53(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, IDENTIFICATION IN THE RAG COMPLEX.
  6. "Stimulation of V(D)J cleavage by high mobility group proteins."
    van Gent D.C., Hiom K., Paull T.T., Gellert M.
    EMBO J. 16:2665-2670(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE RAG COMPLEX.
  7. "Mutational analysis of RAG1 and RAG2 identifies three catalytic amino acids in RAG1 critical for both cleavage steps of V(D)J recombination."
    Landree M.A., Wibbenmeyer J.A., Roth D.B.
    Genes Dev. 13:3059-3069(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF ASP-128; GLU-199; ASP-202; GLU-280; ASP-310; ASP-358 AND ASP-374.
  8. "A direct interaction between the RAG2 C terminus and the core histones is required for efficient V(D)J recombination."
    West K.L., Singha N.C., De Ioannes P., Lacomis L., Erdjument-Bromage H., Tempst P., Cortes P.
    Immunity 23:203-212(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, HISTONE-BINDING, MUTAGENESIS OF TYR-402; ASN-403; ASP-406 AND GLU-407.
  9. Cited for: DOMAIN PHD-TYPE ZINC-FINGER, ZINC-BINDING, HISTONE-BINDING, MUTAGENESIS OF TYR-415; MET-443 AND TRP-453.
  10. "Trex1 prevents cell-intrinsic initiation of autoimmunity."
    Stetson D.B., Ko J.S., Heidmann T., Medzhitov R.
    Cell 134:587-598(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
  11. "H3K4me3 stimulates the V(D)J RAG complex for both nicking and hairpinning in trans in addition to tethering in cis: implications for translocations."
    Shimazaki N., Tsai A.G., Lieber M.R.
    Mol. Cell 34:535-544(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF TRP-453.
  12. Cited for: FUNCTION.
  13. "Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis."
    Yin F.F., Bailey S., Innis C.A., Ciubotaru M., Kamtekar S., Steitz T.A., Schatz D.G.
    Nat. Struct. Mol. Biol. 16:499-508(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RAG1.
  14. Cited for: STRUCTURE BY NMR OF 414-487 IN COMPLEX WITH ZINC, ZINC-BINDING, PHOSPHOINOSITIDE-BINDING, MUTAGENESIS OF LYS-440; ARG-464 AND HIS-468.
  15. "The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2."
    Ramon-Maiques S., Kuo A.J., Carney D., Matthews A.G., Oettinger M.A., Gozani O., Yang W.
    Proc. Natl. Acad. Sci. U.S.A. 104:18993-18998(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 414-487 IN COMPLEX WITH ZINC AND H3 PEPTIDE, DOMAIN PHD-TYPE ZINC-FINGER, ZINC-BINDING, HISTONE-BINDING, MUTAGENESIS OF TYR-445.

Entry informationi

Entry nameiRAG2_MOUSE
AccessioniPrimary (citable) accession number: P21784
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 1991
Last sequence update: July 15, 1998
Last modified: October 29, 2014
This is version 123 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3