PDBsum entry: 2v85

Protein binding

PDB id: 2v85

Contents

Protein chains

74 a.a. *

82 a.a. *

12 a.a. *

Ligands

ALA-NMM-THR-M3L-GLN-THR-ALA-ARG-LYS-ALA

Metals

_ZN ×4

Waters ×173

* Residue conservation analysis

PDB id:

2v85

Name:

Protein binding

Title:

Crystal structure of rag2-phd finger in complex with h3r2me1k4me3 peptide

Structure:

Vdj recombination-activating protein 2. Chain: a, b. Fragment: residues 414-487. Synonym: rag2, rag2-phd finger. Engineered: yes. H3r2me1k4me3 peptide. Chain: d, e. Fragment: h3 (1-21), biotinilated at c-terminus. Other_details: r2 monomethylated and k4 trimethylated

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes

Resolution:

2.00Å R-factor: 0.186 R-free: 0.197

Authors:

S.Ramon-Maiques,W.Yang

Key ref:

S.Ramón-Maiques et al. (2007). The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2. Proc Natl Acad Sci U S A, 104, 18993-18998. PubMed id: 18025461 DOI: 10.1073/pnas.0709170104

Date:

02-Aug-07 Release date: 11-Dec-07

Protein chain

P21784  (RAG2_MOUSE) -  V(D)J recombination-activating protein 2

Seq: 527 a.a.

Struc: 74 a.a.

Protein chain

P21784  (RAG2_MOUSE) -  V(D)J recombination-activating protein 2

Seq: 527 a.a.

Struc: 82 a.a.*

Protein chain

	No UniProt id for this chain
	* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)
• Biological process: DNA recombination (1 term)
• Biochemical function: DNA binding (1 term)

DOI no: 10.1073/pnas.0709170104

Proc Natl Acad Sci U S A 104:18993-18998 (2007)

PubMed id: 18025461

The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2.

S.Ramón-Maiques, A.J.Kuo, D.Carney, A.G.Matthews, M.A.Oettinger, O.Gozani, W.Yang.

ABSTRACT

Recombination activating gene (RAG) 1 and RAG2 together catalyze V(D)J gene rearrangement in lymphocytes as the first step in the assembly and maturation of antigen receptors. RAG2 contains a plant homeodomain (PHD) near its C terminus (RAG2-PHD) that recognizes histone H3 methylated at lysine 4 (H3K4me) and influences V(D)J recombination. We report here crystal structures of RAG2-PHD alone and complexed with five modified H3 peptides. Two aspects of RAG2-PHD are unique. First, in the absence of the modified peptide, a peptide N-terminal to RAG2-PHD occupies the substrate-binding site, which may reflect an autoregulatory mechanism. Second, in contrast to other H3K4me3-binding PHD domains, RAG2-PHD substitutes a carboxylate that interacts with arginine 2 (R2) with a Tyr, resulting in binding to H3K4me3 that is enhanced rather than inhibited by dimethylation of R2. Five residues involved in histone H3 recognition were found mutated in severe combined immunodeficiency (SCID) patients. Disruption of the RAG2-PHD structure appears to lead to the absence of T and B lymphocytes, whereas failure to bind H3K4me3 is linked to Omenn Syndrome. This work provides a molecular basis for chromatin-dependent gene recombination and presents a single protein domain that simultaneously recognizes two distinct histone modifications, revealing added complexity in the read-out of combinatorial histone modifications.

Selected figure(s)

Figure 2.
Fig. 2. Structural comparison of RAG2-PHD with and without the H3 peptide. (A) Superposition of the RAG2-PHD crystal structures in the absence (magenta) and presence of H3K4me3 (green). Residues 471–473 are disordered in the apo form and represented by a dashed lane. The N terminus of the polypeptide chain is indicated. (B) The N-terminal peptide of RAG2-PHD partially occupies the H3-binding groove in the absence of H3 peptide. The molecular surface presentation of RAG2-PHD is shown with the bound H3K4me3 peptide (yellow wire), and superimposed on it is the N-terminal peptide of RAG2-PHD (pink wire) observed in the apo-structure. A proline residue, three residues N-terminal to the first residue of RAG2-PHD (G414), occupies the trimethyl ammonium-binding site.

Figure 5.
Fig. 5. Interactions of RAG2-PHD with different R2 and K4 doubly modified H3 peptides. (A) H3R2me1/K4me3. (B) H3R2me2a/K4me3 (alternate conformations of R2 shown in yellow and orange). (C) H3R2me2s/K4me3. (D) H3R2me2s/K4me2. The RAG2-PHD is shown as green ribbons, and the four key binding residues are shown as magenta ball-and-sticks. The H3 peptide in yellow ball-and-stick is shown with the corresponding 2F[o] – F[c] omit electron density map contoured at 1 .

Figures were selected by an automated process.