P21784 (RAG2_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
V(D)J recombination-activating protein 2
Short name=RAG-2

Gene names

Name:	Rag2
Synonyms:	Rag-2

Organism

Mus musculus (Mouse)

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	527 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.1 Ref.4 Ref.5 Ref.8 Ref.10 Ref.11
Subunit structure	Component of the RAG complex composed of core components RAG1 and RAG2, and associated component HMGB1 or HMGB2.
Subcellular location	Nucleus.
Tissue specificity	Maturing lymphoid cells.
Domain	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). Ref.9 Ref.14
Disruption phenotype	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. Ref.3
Sequence similarities	Belongs to the RAG2 family. Contains 1 PHD-type zinc finger.

Ontologies

Keywords
Biological process	DNA recombination
Cellular component	Nucleus
Domain	Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Chromatin regulator
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	B cell homeostatic proliferation Inferred from mutant phenotype. Source: MGI B cell lineage commitment Inferred from mutant phenotype. Source: MGI T cell differentiation in thymus Inferred from mutant phenotype. Source: UniProtKB T cell lineage commitment Inferred from mutant phenotype. Source: MGI V(D)J recombination Inferred from mutant phenotype Ref.9. Source: UniProtKB chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW positive regulation of organ growth Inferred from mutant phenotype. Source: MGI pre-B cell allelic exclusion Inferred from mutant phenotype Ref.11. Source: UniProtKB
Cellular component	nucleus Inferred by curator Ref.9. Source: UniProtKB
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro chromatin binding Inferred from direct assay Ref.14Ref.9. Source: UniProtKB methylated histone residue binding Inferred from direct assay Ref.14Ref.9. Source: UniProtKB phosphatidylinositol-3,4,5-trisphosphate binding Inferred from direct assay Ref.13. Source: UniProtKB phosphatidylinositol-3,4-bisphosphate binding Inferred from direct assay Ref.13. Source: UniProtKB phosphatidylinositol-3,5-bisphosphate binding Inferred from direct assay Ref.13. Source: UniProtKB phosphatidylinositol-4,5-bisphosphate binding Inferred from direct assay Ref.13. Source: UniProtKB zinc ion binding Inferred from direct assay Ref.13Ref.14Ref.9. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 527

527

V(D)J recombination-activating protein 2

PRO_0000167138

Regions

Zinc finger

416 – 484

69

PHD-type; atypical

Compositional bias

352 – 410

59

Asp/Glu-rich (acidic)

Sites

Metal binding

419

1

Zinc 1

Metal binding

423

1

Zinc 1

Metal binding

446

1

Zinc 2

Metal binding

452

1

Zinc 2

Metal binding

455

1

Zinc 1

Metal binding

458

1

Zinc 1

Metal binding

478

1

Zinc 2

Metal binding

481

1

Zinc 2

Experimental info

Mutagenesis

128

1

D → N: Does not affect the endonuclease activity of the RAG complex. Ref.7

Mutagenesis

199

1

E → Q: Does not affect the endonuclease activity of the RAG complex. Ref.7

Mutagenesis

202

1

D → N: Does not affect the endonuclease activity of the RAG complex. Ref.7

Mutagenesis

280

1

E → Q: Does not affect the endonuclease activity of the RAG complex. Ref.7

Mutagenesis

310

1

D → N: Does not affect the endonuclease activity of the RAG complex. Ref.7

Mutagenesis

358

1

D → N: Does not affect the endonuclease activity of the RAG complex. Ref.7

Mutagenesis

374

1

D → N: Does not affect the endonuclease activity of the RAG complex. Ref.7

Mutagenesis

402

1

Y → A: Reduced interaction with histones. Ref.8

Mutagenesis

403

1

N → A: Reduced interaction with histones. Ref.8

Mutagenesis

406

1

D → A: Reduced interaction with histones. Ref.8

Mutagenesis

407

1

E → A: Reduced interaction with histones. Ref.8

Mutagenesis

408

1

D → A: Induces a slight reduction in V(D)J recombination without affecting interaction with histones.

Mutagenesis

415

1

Y → A: Abolishes binding to H3K4me3 without affecting phosphoinositide-binding. Ref.9

Mutagenesis

440

1

K → A: Binds PtdIns(4,5)P2 at wild-type level. Ref.13

Mutagenesis

443

1

M → A: Abolishes binding to H3K4me3 without affecting phosphoinositide-binding. Ref.9

Mutagenesis

445

1

Y → A or D: Still binds H3K4me3 and H3R2me2 but with reduced affinity. Ref.14

Mutagenesis

453

1

W → R: Abolishes binding to H3K4me3 without affecting phosphoinositide-binding. Impairs enzymatic activity of the RAG complex. Ref.9 Ref.10

Mutagenesis

464

1

R → A: Leads to a strong reduction in PtdIns(4,5)P2-binding. Ref.13

Mutagenesis

468

1

H → A: Leads to a strong reduction in PtdIns(4,5)P2-binding. Ref.13

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

527

Helix Strand Turn

Details...

Turn

427 – 429

3

Beta strand

438 – 440

3

Beta strand

443 – 446

4

Beta strand

452 – 455

4

Helix

456 – 459

4

Helix

463 – 471

9

Turn

479 – 481

3

Sequences

	Sequence		Length	Mass (Da)
	P21784 [UniParc]. Last modified July 15, 1998. Version 2. Checksum: 51086F95A4A664A7	FASTA	527	59,074
	10 20 30 40 50 60 MSLQMVTVGH NIALIQPGFS LMNFDGQVFF FGQKGWPKRS CPTGVFHFDI KQNHLKLKPA 70 80 90 100 110 120 IFSKDSCYLP PLRYPATCSY KGSIDSDKHQ YIIHGGKTPN NELSDKIYIM SVACKNNKKV 130 140 150 160 170 180 TFRCTEKDLV GDVPEPRYGH SIDVVYSRGK SMGVLFGGRS YMPSTQRTTE KWNSVADCLP 190 200 210 220 230 240 HVFLIDFEFG CATSYILPEL QDGLSFHVSI ARNDTVYILG GHSLASNIRP ANLYRIRVDL 250 260 270 280 290 300 PLGTPAVNCT VLPGGISVSS AILTQTNNDE FVIVGGYQLE NQKRMVCSLV SLGDNTIEIS 310 320 330 340 350 360 EMETPDWTSD IKHSKIWFGS NMGNGTIFLG IPGDNKQAMS EAFYFYTLRC SEEDLSEDQK 370 380 390 400 410 420 IVSNSQTSTE DPGDSTPFED SEEFCFSAEA TSFDGDDEFD TYNEDDEDDE SVTGYWITCC 430 440 450 460 470 480 PTCDVDINTW VPFYSTELNK PAMIYCSHGD GHWVHAQCMD LEERTLIHLS EGSNKYYCNE 490 500 510 520 HVQIARALQT PKRNPPLQKP PMKSLHKKGS GKVLTPAKKS FLRRLFD

References

[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: 2360047] [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: 1547487] [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: 8521468] [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: 9094713] [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: 9184213] [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: 10601032] [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: 16111638] [Abstract] Cited for: FUNCTION, HISTONE-BINDING, MUTAGENESIS OF TYR-402; ASN-403; ASP-406 AND GLU-407.
[9]	"RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination." Matthews A.G., Kuo A.J., Ramon-Maiques S., Han S., Champagne K.S., Ivanov D., Gallardo M., Carney D., Cheung P., Ciccone D.N., Walter K.L., Utz P.J., Shi Y., Kutateladze T.G., Yang W., Gozani O., Oettinger M.A. Nature 450:1106-1110(2007) [PubMed: 18033247] [Abstract] Cited for: DOMAIN PHD-TYPE ZINC FINGER, ZINC-BINDING, HISTONE-BINDING, MUTAGENESIS OF TYR-415; MET-443 AND TRP-453.
[10]	"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: 19524534] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF TRP-453.
[11]	"RAG-1 and ATM coordinate monoallelic recombination and nuclear positioning of immunoglobulin loci." Hewitt S.L., Yin B., Ji Y., Chaumeil J., Marszalek K., Tenthorey J., Salvagiotto G., Steinel N., Ramsey L.B., Ghysdael J., Farrar M.A., Sleckman B.P., Schatz D.G., Busslinger M., Bassing C.H., Skok J.A. Nat. Immunol. 10:655-664(2009) [PubMed: 19448632] [Abstract] Cited for: FUNCTION.
[12]	"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: 19396172] [Abstract] Cited for: INTERACTION WITH RAG1.
[13]	"A PHD finger motif in the C terminus of RAG2 modulates recombination activity." Elkin S.K., Ivanov D., Ewalt M., Ferguson C.G., Hyberts S.G., Sun Z.Y., Prestwich G.D., Yuan J., Wagner G., Oettinger M.A., Gozani O.P. J. Biol. Chem. 280:28701-28710(2005) [PubMed: 15964836] [Abstract] 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.
[14]	"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: 18025461] [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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M64796 mRNA. Translation: AAB82302.1.

IPI

IPI00127759.

PIR

A34852.

RefSeq

NP_033046.1. NM_009020.3.

UniGene

Mm.4988.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P21784.

SMR

P21784. Positions 130-226, 414-487.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-46179N.

STRING

P21784.

PTM databases

PhosphoSite

P21784.

Proteomic databases

PRIDE

P21784.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSMUST00000044031; ENSMUSP00000038204; ENSMUSG00000032864.
ENSMUST00000111227; ENSMUSP00000106858; ENSMUSG00000032864.

GeneID

19374.

KEGG

mmu:19374.

Organism-specific databases

CTD

5897.

MGI

MGI:97849. Rag2.

Phylogenomic databases

eggNOG

maNOG10276.

HOGENOM

HBG713661.

HOVERGEN

HBG006694.

InParanoid

P21784.

OMA

GHWVHAQ.

OrthoDB

EOG44XJGJ.

PhylomeDB

P21784.

Gene expression databases

ArrayExpress

P21784.

Bgee

P21784.

CleanEx

MM_RAG2.

Genevestigator

P21784.

GermOnline

ENSMUSG00000032864. Mus musculus.

Family and domain databases

InterPro

IPR011043. Gal_Oxase/kelch_b-propeller.
IPR015915. Kelch-typ_b-propeller.
IPR004321. RAG2.
[Graphical view]

Gene3D

G3DSA:2.120.10.80. Kelch-typ_b-propeller. 1 hit.

KO

K10988.

PANTHER

PTHR10960. RAG2. 1 hit.

Pfam

PF03089. RAG2. 1 hit.
[Graphical view]

SUPFAM

SSF50965. Gal_oxid_central. 1 hit.

PROSITE

PS01359. ZF_PHD_1. False negative.
PS50016. ZF_PHD_2. False negative.
[Graphical view]

ProtoNet

Search...

Other

NextBio

296467.

SOURCE

Search...

Entry information

Entry name

RAG2_MOUSE

Accession

Primary (citable) accession number: P21784

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 1, 1991
Last sequence update:	July 15, 1998
Last modified:	November 16, 2011
This is version 97 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program