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75  structures 230  species 0  interactions 279  sequences 18  architectures

Family: RAG1 (PF12940)

Summary: Recombination-activation protein 1 (RAG1), recombinase

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Recombination-activation protein 1 (RAG1), recombinase Provide feedback

This family is one of the two different components of the RAG1-RAG2 V(D)J recombinase complex. The RAG complex, consisting of two RAG1 and two RAG2 proteins is a multi-protein complex that mediates DNA cleavage during V(D)J (variable-diversity-joining) recombination [2]. RAG1 mediates DNA-binding to the conserved recombination signal sequences (RSS) [3]. Many of the proteins in this family are fragments. Solution of the structure of the complex of RAG1 and RAG2 shows that each protein dimerises with itself and each pair then complexes together to from the RAG1-RAG2 V(D)J recombinase enzyme. The different structural elements in RAG1 for UniProtKB:P15919 are: an N-terminal nonamer-binding domain from residues 391-459; a dimerisation and DNA-binding domain from 459-515; an extended pre-RNase H domain from 515-588; the catalytic RNase H domain from 588-719; a ZnC2 domain from 719-791; and ZnH2 domain from 791-962; and a three-helix C-terminal domain from 962-1008 [4,5].

Literature references

  1. Hansen JD, Kaattari SL;, Immunogenetics. 1995;42:188-195.: The recombination activation gene 1 (RAG1) of rainbow trout (Oncorhynchus mykiss): cloning, expression, and phylogenetic analysis. PUBMED:7642230 EPMC:7642230

  2. Matthews AG, Oettinger MA;, Nat Immunol. 2009;10:817-821.: RAG: a recombinase diversified. PUBMED:19621044 EPMC:19621044

  3. Difilippantonio MJ, McMahan CJ, Eastman QM, Spanopoulou E, Schatz DG;, Cell. 1996;87:253-262.: RAG1 mediates signal sequence recognition and recruitment of RAG2 in V(D)J recombination. PUBMED:8861909 EPMC:8861909

  4. Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM;, Nucleic Acids Res. 2014;42:4160-4179.: The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification. PUBMED:24464998 EPMC:24464998

  5. Kim MS, Lapkouski M, Yang W, Gellert M;, Nature. 2015;518:507-511.: Crystal structure of the V(D)J recombinase RAG1-RAG2. PUBMED:25707801 EPMC:25707801

This tab holds annotation information from the InterPro database.

InterPro entry IPR024627

The development of B and T cells depends on the rearrangement of variable (V), diversity (D), and joining (J) gene segments to produce mature Ig and T cell receptor coding regions. This rearrangement process, known as V(D)J recombination is initiated by a complex consisting of multi-domain proteins RAG1 and RAG2. The RAG proteins catalyse DNA cleavage in the first phase of the reaction using a recombination signal sequence (RSS) that flanks V, D and J segments [ PUBMED:9228952 , PUBMED:14671314 , PUBMED:22796426 ].

Recombination activating protein 1 (RAG1) is the catalytic component of the RAG complex [ PUBMED:19621044 ]. RAG1 contains a RING finger domain that can act as a ubiquitin ligase (E3), and can promote its own ubiquitylation and targets both karyopherin alpha 1 (KPNA1) and histone 3 (H3) [ PUBMED:19118899 , PUBMED:21256161 ].

Many of the proteins recognised by this entry are fragments.

Gene Ontology

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Domain organisation

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Seed source: jackhmmer:Q6U1Q1
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mistry J , Eberhardt R
Number in seed: 2
Number in full: 279
Average length of the domain: 597.40 aa
Average identity of full alignment: 76 %
Average coverage of the sequence by the domain: 61.86 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 26.0 28.0
Noise cut-off 24.8 22.3
Model length: 651
Family (HMM) version: 10
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Species distribution

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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the RAG1 domain has been found. There are 75 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
G3V6K9 View 3D Structure Click here
O13033 View 3D Structure Click here
P15918 View 3D Structure Click here
P15919 View 3D Structure Click here