PDBsum entry 2v88

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protein ligands metals Protein-protein interface(s) links
Protein binding PDB id
Protein chains
78 a.a. *
_ZN ×4
Waters ×227
* Residue conservation analysis
PDB id:
Name: Protein binding
Title: Crystal structure of rag2-phd finger in complex with h3r2me2sk4me2 peptide
Structure: Vdj recombination-activating protein 2. Chain: a, b. Fragment: residues 414-487. Synonym: rag2, rag2-phd finger. Engineered: yes. H3r2me2sk4me3 peptide. Chain: d, f. Fragment: h3 (1-21), biotinylated at c-terminus. Other_details: symmetric di-methylated r2 and
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes
2.00Å     R-factor:   0.195     R-free:   0.231
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
03-Aug-07     Release date:   11-Dec-07    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P21784  (RAG2_MOUSE) -  V(D)J recombination-activating protein 2
527 a.a.
78 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23211769 C.A.Musselman, M.E.Lalonde, J.Côté, and T.G.Kutateladze (2012).
Perceiving the epigenetic landscape through histone readers.
  Nat Struct Mol Biol, 19, 1218-1227.  
21219174 M.Gostissa, F.W.Alt, and R.Chiarle (2011).
Mechanisms that promote and suppress chromosomal translocations in lymphocytes.
  Annu Rev Immunol, 29, 319-350.  
21243721 O.Binda, M.Boyce, J.S.Rush, K.K.Palaniappan, C.R.Bertozzi, and O.Gozani (2011).
A chemical method for labeling lysine methyltransferase substrates.
  Chembiochem, 12, 330-334.  
21167713 S.M.Fuchs, K.Krajewski, R.W.Baker, V.L.Miller, and B.D.Strahl (2011).
Influence of combinatorial histone modifications on antibody and effector protein recognition.
  Curr Biol, 21, 53-58.  
21243717 S.S.Oliver, and J.M.Denu (2011).
Dynamic interplay between histone H3 modifications and protein interpreters: emerging evidence for a "histone language".
  Chembiochem, 12, 299-307.  
20116856 A.Bhattacharyya, and J.M.Jones (2010).
Requirement for ubiquitin conjugation and 26S proteasome activity at an early stage in V(D)J recombination.
  Mol Immunol, 47, 1173-1180.  
20190764 A.L.Garske, S.S.Oliver, E.K.Wagner, C.A.Musselman, G.LeRoy, B.A.Garcia, T.G.Kutateladze, and J.M.Denu (2010).
Combinatorial profiling of chromatin binding modules reveals multisite discrimination.
  Nat Chem Biol, 6, 283-290.  
20234091 C.Couëdel, C.Roman, A.Jones, P.Vezzoni, A.Villa, and P.Cortes (2010).
Analysis of mutations from SCID and Omenn syndrome patients reveals the central role of the Rag2 PHD domain in regulating V(D)J recombination.
  J Clin Invest, 120, 1337-1344.  
20727027 C.Vettermann, and M.S.Schlissel (2010).
Allelic exclusion of immunoglobulin genes: models and mechanisms.
  Immunol Rev, 237, 22-42.  
21149691 G.J.Grundy, W.Yang, and M.Gellert (2010).
Autoinhibition of DNA cleavage mediated by RAG1 and RAG2 is overcome by an epigenetic signal in V(D)J recombination.
  Proc Natl Acad Sci U S A, 107, 22487-22492.  
20923397 K.L.Yap, and M.M.Zhou (2010).
Keeping it in the family: diverse histone recognition by conserved structural folds.
  Crit Rev Biochem Mol Biol, 45, 488-505.  
20613843 L.Zeng, Q.Zhang, S.Li, A.N.Plotnikov, M.J.Walsh, and M.M.Zhou (2010).
Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b.
  Nature, 466, 258-262.
PDB codes: 2kwj 2kwk 2kwn 2kwo
20953165 R.A.Varier, N.S.Outchkourov, Graaf, F.M.van Schaik, H.J.Ensing, F.Wang, J.M.Higgins, G.J.Kops, and H.T.Timmers (2010).
A phospho/methyl switch at histone H3 regulates TFIID association with mitotic chromosomes.
  EMBO J, 29, 3967-3978.  
20864355 R.Subrahmanyam, and R.Sen (2010).
RAGs' eye view of the immunoglobulin heavy chain gene locus.
  Semin Immunol, 22, 337-345.  
20004590 S.D.Fugmann (2010).
The origins of the Rag genes--from transposition to V(D)J recombination.
  Semin Immunol, 22, 10-16.  
21036059 S.Desiderio (2010).
Temporal and spatial regulatory functions of the V(D)J recombinase.
  Semin Immunol, 22, 362-369.  
20829066 S.Spicuglia, A.Pekowska, J.Zacarias-Cabeza, and P.Ferrier (2010).
Epigenetic control of Tcrb gene rearrangement.
  Semin Immunol, 22, 330-336.  
20832333 Y.Bergman, and H.Cedar (2010).
Epigenetic control of recombination in the immune system.
  Semin Immunol, 22, 323-329.  
20728025 Y.Zhang, M.Gostissa, D.G.Hildebrand, M.S.Becker, C.Boboila, R.Chiarle, S.Lewis, and F.W.Alt (2010).
The role of mechanistic factors in promoting chromosomal translocations found in lymphoid and other cancers.
  Adv Immunol, 106, 93.  
19621044 A.G.Matthews, and M.A.Oettinger (2009).
RAG: a recombinase diversified.
  Nat Immunol, 10, 817-821.  
19624289 C.A.Musselman, R.E.Mansfield, A.L.Garske, F.Davrazou, A.H.Kwan, S.S.Oliver, H.O'Leary, J.M.Denu, J.P.Mackay, and T.G.Kutateladze (2009).
Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications.
  Biochem J, 423, 179-187.  
20048137 C.A.Musselman, and T.G.Kutateladze (2009).
PHD fingers: epigenetic effectors and potential drug targets.
  Mol Interv, 9, 314-323.  
19392692 C.L.Thomas, D.Schmidt, E.M.Bayer, R.Dreos, and A.J.Maule (2009).
Arabidopsis plant homeodomain finger proteins operate downstream of auxin accumulation in specifying the vasculature and primary root meristem.
  Plant J, 59, 426-436.  
19956676 D.J.Bua, A.J.Kuo, P.Cheung, C.L.Liu, V.Migliori, A.Espejo, F.Casadio, C.Bassi, B.Amati, M.T.Bedford, E.Guccione, and O.Gozani (2009).
Epigenome microarray platform for proteome-wide dissection of chromatin-signaling networks.
  PLoS One, 4, e6789.  
19293276 F.Chignola, M.Gaetani, A.Rebane, T.Org, L.Mollica, C.Zucchelli, A.Spitaleri, V.Mannella, P.Peterson, and G.Musco (2009).
The solution structure of the first PHD finger of autoimmune regulator in complex with non-modified histone H3 tail reveals the antagonistic role of H3R2 methylation.
  Nucleic Acids Res, 37, 2951-2961.
PDB code: 2ke1
19242715 I.S.Zakharova, A.I.Shevchenko, and S.M.Zakian (2009).
Monoallelic gene expression in mammals.
  Chromosoma, 118, 279-290.  
19333736 J.M.Jones, and C.Simkus (2009).
The roles of the RAG1 and RAG2 "non-core" regions in V(D)J recombination and lymphocyte development.
  Arch Immunol Ther Exp (Warsz), 57, 105-116.  
19752184 K.Beck, M.M.Peak, T.Ota, D.Nemazee, and C.Murre (2009).
Distinct roles for E12 and E47 in B cell specification and the sequential rearrangement of immunoglobulin light chain loci.
  J Exp Med, 206, 2271-2284.  
19442115 K.S.Champagne, and T.G.Kutateladze (2009).
Structural insight into histone recognition by the ING PHD fingers.
  Curr Drug Targets, 10, 432-441.  
19234526 M.A.Adams-Cioaba, and J.Min (2009).
Structure and function of histone methylation binding proteins.
  Biochem Cell Biol, 87, 93.  
19362589 M.J.Hitchler, and F.E.Domann (2009).
Metabolic defects provide a spark for the epigenetic switch in cancer.
  Free Radic Biol Med, 47, 115-127.  
19150423 M.T.Bedford, and S.G.Clarke (2009).
Protein arginine methylation in mammals: who, what, and why.
  Mol Cell, 33, 1.  
19524534 N.Shimazaki, A.G.Tsai, and M.R.Lieber (2009).
H3K4me3 stimulates the V(D)J RAG complex for both nicking and hairpinning in trans in addition to tethering in cis: implications for translocations.
  Mol Cell, 34, 535-544.  
19317649 O.J.Rando, and H.Y.Chang (2009).
Genome-wide views of chromatin structure.
  Annu Rev Biochem, 78, 245-271.  
19234465 Q.Zhao, G.Rank, Y.T.Tan, H.Li, R.L.Moritz, R.J.Simpson, L.Cerruti, D.J.Curtis, D.J.Patel, C.D.Allis, J.M.Cunningham, and S.M.Jane (2009).
PRMT5-mediated methylation of histone H4R3 recruits DNMT3A, coupling histone and DNA methylation in gene silencing.
  Nat Struct Mol Biol, 16, 304-311.  
19324890 R.Maitra, and M.J.Sadofsky (2009).
A WW-like module in the RAG1 N-terminal domain contributes to previously unidentified protein-protein interactions.
  Nucleic Acids Res, 37, 3301-3309.  
19446523 S.Chakravarty, L.Zeng, and M.M.Zhou (2009).
Structure and site-specific recognition of histone H3 by the PHD finger of human autoimmune regulator.
  Structure, 17, 670-679.
PDB code: 2kft
18923809 S.S.Ng, W.W.Yue, U.Oppermann, and R.J.Klose (2009).
Dynamic protein methylation in chromatin biology.
  Cell Mol Life Sci, 66, 407-422.  
  19731809 Y.Liu, L.Zhang, and S.Desiderio (2009).
Temporal and spatial regulation of V(D)J recombination: interactions of extrinsic factors with the RAG complex.
  Adv Exp Med Biol, 650, 157-165.  
18633479 A.J.Bowen, and A.E.Corcoran (2008).
How chromatin remodelling allows shuffling of immunoglobulin heavy chain genes.
  Mol Biosyst, 4, 790-798.  
18508253 A.Shilatifard (2008).
Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation.
  Curr Opin Cell Biol, 20, 341-348.  
18403192 A.Villa, V.Marrella, F.Rucci, and L.D.Notarangelo (2008).
Genetically determined lymphopenia and autoimmune manifestations.
  Curr Opin Immunol, 20, 318-324.  
18499250 D.R.Wilson, D.D.Norton, and S.D.Fugmann (2008).
The PHD domain of the sea urchin RAG2 homolog, SpRAG2L, recognizes dimethylated lysine 4 in histone H3 tails.
  Dev Comp Immunol, 32, 1221-1230.  
18400481 H.Cedar, and Y.Bergman (2008).
Choreography of Ig allelic exclusion.
  Curr Opin Immunol, 20, 308-317.  
18682226 H.van Ingen, F.M.van Schaik, H.Wienk, J.Ballering, H.Rehmann, A.C.Dechesne, J.A.Kruijzer, R.M.Liskamp, H.T.Timmers, and R.Boelens (2008).
Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3.
  Structure, 16, 1245-1256.  
18623064 K.S.Champagne, N.Saksouk, P.V.Peña, K.Johnson, M.Ullah, X.J.Yang, J.Côté, and T.G.Kutateladze (2008).
The crystal structure of the ING5 PHD finger in complex with an H3K4me3 histone peptide.
  Proteins, 72, 1371-1376.
PDB code: 3c6w
18682256 L.A.Baker, C.D.Allis, and G.G.Wang (2008).
PHD fingers in human diseases: disorders arising from misinterpreting epigenetic marks.
  Mutat Res, 647, 3.  
18488044 L.Zeng, K.L.Yap, A.V.Ivanov, X.Wang, S.Mujtaba, O.Plotnikova, F.J.Rauscher, and M.M.Zhou (2008).
Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing.
  Nat Struct Mol Biol, 15, 626-633.
PDB code: 2ro1
18498752 M.Fiedler, M.J.Sánchez-Barrena, M.Nekrasov, J.Mieszczanek, V.Rybin, J.Müller, P.Evans, and M.Bienz (2008).
Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex.
  Mol Cell, 30, 507-518.
PDB codes: 2vp7 2vpb 2vpd 2vpe 2vpg
18765789 M.Lange, B.Kaynak, U.B.Forster, M.Tönjes, J.J.Fischer, C.Grimm, J.Schlesinger, S.Just, I.Dunkel, T.Krueger, S.Mebus, H.Lehrach, R.Lurz, J.Gobom, W.Rottbauer, S.Abdelilah-Seyfried, and S.Sperling (2008).
Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex.
  Genes Dev, 22, 2370-2384.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.