spacer
spacer

PDBsum entry 2gf7
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Metal binding protein PDB id
2gf7

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
115 a.a. *
Ligands
SO4 ×4
Waters ×200
* Residue conservation analysis
PDB id:
2gf7
Name: Metal binding protein
Title: Double tudor domain structure
Structure: Jumonji domain-containing protein 2a. Chain: a, b, c, d. Fragment: double tudor domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: jmjd2a, jmjd2, kiaa0677. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.20Å     R-factor:   0.225     R-free:   0.264
Authors: Y.Huang,J.Fang,M.T.Bedford,Y.Zhang,R.M.Xu
Key ref:
Y.Huang et al. (2006). Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science, 312, 748-751. PubMed id: 16601153 DOI: 10.1126/science.1125162
Date:
21-Mar-06     Release date:   02-May-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O75164  (KDM4A_HUMAN) -  Lysine-specific demethylase 4A from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1064 a.a.
115 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 2: E.C.1.14.11.66  - [histone H3]-trimethyl-L-lysine(9) demethylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: N6,N6,N6-trimethyl-L-lysyl9-[histone H3] + 2 2-oxoglutarate + 2 O2 = N6-methyl-L-lysyl9-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2
N(6),N(6),N(6)-trimethyl-L-lysyl(9)-[histone H3]
 + 2 × 2-oxoglutarate
 + 2 × O2
 = N(6)-methyl-L-lysyl(9)-[histone H3]
 + 2 × formaldehyde
 + 2 × succinate
 + 2 × CO2
   Enzyme class 3: E.C.1.14.11.69  - [histone H3]-trimethyl-L-lysine(36) demethylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: N6,N6,N6-trimethyl-L-lysyl36-[histone H3] + 2 2-oxoglutarate + 2 O2 = N6-methyl-L-lysyl36-[histone H3] + 2 formaldehyde + 2 succinate + 2 CO2
N(6),N(6),N(6)-trimethyl-L-lysyl(36)-[histone H3]
 + 2 × 2-oxoglutarate
 + 2 × O2
 = N(6)-methyl-L-lysyl(36)-[histone H3]
 + 2 × formaldehyde
 + 2 × succinate
 + 2 × CO2
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1126/science.1125162 Science 312:748-751 (2006)
PubMed id: 16601153  
 
 
Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A.
Y.Huang, J.Fang, M.T.Bedford, Y.Zhang, R.M.Xu.
 
  ABSTRACT  
 
Biological responses to histone methylation critically depend on the faithful readout and transduction of the methyl-lysine signal by "effector" proteins, yet our understanding of methyl-lysine recognition has so far been limited to the study of histone binding by chromodomain and WD40-repeat proteins. The double tudor domain of JMJD2A, a Jmjc domain-containing histone demethylase, binds methylated histone H3-K4 and H4-K20. We found that the double tudor domain has an interdigitated structure, and the unusual fold is required for its ability to bind methylated histone tails. The cocrystal structure of the JMJD2A double tudor domain with a trimethylated H3-K4 peptide reveals that the trimethyl-K4 is bound in a cage of three aromatic residues, two of which are from the tudor-2 motif, whereas the binding specificity is determined by side-chain interactions involving amino acids from the tudor-1 motif. Our study provides mechanistic insights into recognition of methylated histone tails by tudor domains and reveals the structural intricacy of methyl-lysine recognition by two closely spaced effector domains.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. JMJD2A structure. (A) A schematic drawing of the domain structure of JMJD2A. (B) Alignment of the double tudor domain sequences of three human JMJD2 homologs, one from zebrafish (Ensemble ID: DARP00000024692) and another from frog (Ensemble ID: XETP00000001152), and human 53BP1. Secondary-structure elements (orange and green for the first and second tudor motifs, respectively), their nomenclature, and the amino acid numbering of JMJD2A are shown above the sequences. The secondary-structure elements of the 53BP1 double tudor domain are delineated below the sequences. JMJD2A residues subjected to mutational studies are indicated by stars. (C) The structure of the JMJD2A double tudor domain (ribbon representation) in complex with a trimethylated H3K4 peptide (ball-and-stick model). Regions spanning the first and second tudor motifs are colored orange and green, respectively. The dotted line indicates a segment of seven disordered residues. (D) The structure of the double tudor domain of 53BP1 shown in a ribbon representation. Secondary-structure elements in (C) and (D) are colored as in (B). 		Figure 2.
Fig. 2. JMJD2A double tudor domain-H3K4Me3 peptide interactions. (A) The double tudor domain as seen in a surface representation with electrostatic potential distribution colored red for negatively charged, white for neutral, and blue for positively charged areas. The peptide is shown as a stick model superimposed with the surrounding 2F[o] - F[c] electron density map (displayed at 1.2 contour level). (B) A stereo view of the methyl-H3K4 (colored cyan) bindingaromaticcagesuperimposedwiththe methyllysine binding aromatic cage of the chromo domain of HP1 (gray). Tudor-1 and Tudor-2 residues are colored orange and green, respectively. (C) A detailed view of JMJD2A-H3K4Me3 interactions. The peptide and the HTD-2 residues involved are shown in a stick model. Dashed lines indicate hydrogen bonds. The same coloring scheme as in Fig. 1 is used.
 
  The above figures are reprinted by permission from the AAAs: Science (2006, 312, 748-751) copyright 2006.  
  Figures were selected by the author.  

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.  
23142980 C.A.Musselman, N.Avvakumov, R.Watanabe, C.G.Abraham, M.E.Lalonde, Z.Hong, C.Allen, S.Roy, J.K.Nuñez, J.Nickoloff, C.A.Kulesza, A.Yasui, J.Côté, and T.G.Kutateladze (2012).
Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1.
  Nat Struct Mol Biol, 19, 1266-1272.
PDB code: 4hcz
23104054 C.Ballaré, M.Lange, A.Lapinaite, G.M.Martin, L.Morey, G.Pascual, R.Liefke, B.Simon, Y.Shi, O.Gozani, T.Carlomagno, S.A.Benitah, and L.Di Croce (2012).
Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity.
  Nat Struct Mol Biol, 19, 1257-1265.
PDB code: 4bd3
22473383 E.L.Greer, and Y.Shi (2012).
Histone methylation: a dynamic mark in health, disease and inheritance.
  Nat Rev Genet, 13, 343-357.  
22864287 G.Cui, S.Park, A.I.Badeaux, D.Kim, J.Lee, J.R.Thompson, F.Yan, S.Kaneko, Z.Yuan, M.V.Botuyan, M.T.Bedford, J.Q.Cheng, and G.Mer (2012).
PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53.
  Nat Struct Mol Biol, 19, 916-924.
PDB codes: 2ldm 3p8d 3sd4
21321607 A.J.Bannister, and T.Kouzarides (2011).
Regulation of chromatin by histone modifications.
  Cell Res, 21, 381-395.  
  21141727 A.K.Upadhyay, and X.Cheng (2011).
Dynamics of histone lysine methylation: structures of methyl writers and erasers.
  Prog Drug Res, 67, 107-124.  
21193996 A.Kaldis, D.Tsementzi, O.Tanriverdi, and K.E.Vlachonasios (2011).
Arabidopsis thaliana transcriptional co-activators ADA2b and SGF29a are implicated in salt stress responses.
  Planta, 233, 749-762.  
21915143 C.Chen, T.J.Nott, J.Jin, and T.Pawson (2011).
Deciphering arginine methylation: Tudor tells the tale.
  Nat Rev Mol Cell Biol, 12, 629-642.  
21297639 J.H.Chang, S.Xiang, K.Xiang, J.L.Manley, and L.Tong (2011).
Structural and biochemical studies of the 5'→3' exoribonuclease Xrn1.
  Nat Struct Mol Biol, 18, 270-276.
PDB codes: 3pie 3pif
21272588 K.E.Gardner, C.D.Allis, and B.D.Strahl (2011).
OPERating ON Chromatin, a Colorful Language where Context Matters.
  J Mol Biol, 409, 36-46.  
22101937 K.Tripsianes, T.Madl, M.Machyna, D.Fessas, C.Englbrecht, U.Fischer, K.M.Neugebauer, and M.Sattler (2011).
Structural basis for dimethylarginine recognition by the Tudor domains of human SMN and SPF30 proteins.
  Nat Struct Mol Biol, 18, 1414-1420.
PDB codes: 4a4e 4a4f 4a4g 4a4h
21333655 M.Attia, A.Förster, C.Rachez, P.Freemont, P.Avner, and U.C.Rogner (2011).
Interaction between nucleosome assembly protein 1-like family members.
  J Mol Biol, 407, 647-660.  
20669242 A.Friberg, A.Oddone, T.Klymenko, J.Müller, and M.Sattler (2010).
Structure of an atypical Tudor domain in the Drosophila Polycomblike protein.
  Protein Sci, 19, 1906-1916.
PDB code: 2xk0
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.  
19897549 A.M.Quinn, M.T.Bedford, A.Espejo, A.Spannhoff, C.P.Austin, U.Oppermann, and A.Simeonov (2010).
A homogeneous method for investigation of methylation-dependent protein-protein interactions in epigenetics.
  Nucleic Acids Res, 38, e11.  
20826339 F.He, T.Umehara, K.Saito, T.Harada, S.Watanabe, T.Yabuki, T.Kigawa, M.Takahashi, K.Kuwasako, K.Tsuda, T.Matsuda, M.Aoki, E.Seki, N.Kobayashi, P.Güntert, S.Yokoyama, and Y.Muto (2010).
Structural insight into the zinc finger CW domain as a histone modification reader.
  Structure, 18, 1127-1139.
PDB codes: 2e61 2rr4
20713507 H.Liu, J.Y.Wang, Y.Huang, Z.Li, W.Gong, R.Lehmann, and R.M.Xu (2010).
Structural basis for methylarginine-dependent recognition of Aubergine by Tudor.
  Genes Dev, 24, 1876-1881.
PDB codes: 3nth 3nti 3ntk
20305267 I.Callebaut, and J.P.Mornon (2010).
LOTUS, a new domain associated with small RNA pathways in the germline.
  Bioinformatics, 26, 1140-1144.  
21168767 I.K.Leung, T.J.Krojer, G.T.Kochan, L.Henry, F.von Delft, T.D.Claridge, U.Oppermann, M.A.McDonough, and C.J.Schofield (2010).
Structural and mechanistic studies on γ-butyrobetaine hydroxylase.
  Chem Biol, 17, 1316-1324.  
20581860 J.Paggetti, A.Largeot, R.Aucagne, A.Jacquel, B.Lagrange, X.J.Yang, E.Solary, J.N.Bastie, and L.Delva (2010).
Crosstalk between leukemia-associated proteins MOZ and MLL regulates HOX gene expression in human cord blood CD34+ cells.
  Oncogene, 29, 5019-5031.  
20023638 J.R.Horton, A.K.Upadhyay, H.H.Qi, X.Zhang, Y.Shi, and X.Cheng (2010).
Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases.
  Nat Struct Mol Biol, 17, 38-43.
PDB codes: 3kv4 3kv5 3kv6 3kv9 3kva 3kvb
20345412 K.Baar (2010).
Epigenetic control of skeletal muscle fibre type.
  Acta Physiol (Oxf), 199, 477-487.  
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.  
20937909 K.Liu, C.Chen, Y.Guo, R.Lam, C.Bian, C.Xu, D.Y.Zhao, J.Jin, F.MacKenzie, T.Pawson, and J.Min (2010).
Structural basis for recognition of arginine methylated Piwi proteins by the extended Tudor domain.
  Proc Natl Acad Sci U S A, 107, 18398-18403.
PDB codes: 3omc 3omg
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
20131086 M.Dalvai, and K.Bystricky (2010).
The role of histone modifications and variants in regulating gene expression in breast cancer.
  J Mammary Gland Biol Neoplasia, 15, 19-33.  
20204433 M.N.Cruickshank, P.Besant, and D.Ulgiati (2010).
The impact of histone post-translational modifications on developmental gene regulation.
  Amino Acids, 39, 1087-1105.  
20373914 N.Mosammaparast, and Y.Shi (2010).
Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases.
  Annu Rev Biochem, 79, 155-179.  
21036059 S.Desiderio (2010).
Temporal and spatial regulatory functions of the V(D)J recombinase.
  Semin Immunol, 22, 362-369.  
21124763 S.Pu, A.L.Turinsky, J.Vlasblom, T.On, X.Xiong, A.Emili, Z.Zhang, J.Greenblatt, J.Parkinson, and S.J.Wodak (2010).
Expanding the landscape of chromatin modification (CM)-related functional domains and genes in human.
  PLoS One, 5, e14122.  
19943104 W.Jin, L.Chen, Y.Chen, S.G.Xu, G.H.Di, W.J.Yin, J.Wu, and Z.M.Shao (2010).
UHRF1 is associated with epigenetic silencing of BRCA1 in sporadic breast cancer.
  Breast Cancer Res Treat, 123, 359-373.  
20210320 X.Cheng, and R.M.Blumenthal (2010).
Coordinated chromatin control: structural and functional linkage of DNA and histone methylation.
  Biochemistry, 49, 2999-3008.  
20141135 X.Li, and T.M.Kapoor (2010).
Approach to profile proteins that recognize post-translationally modified histone "tails".
  J Am Chem Soc, 132, 2504-2505.  
20068219 X.Li, X.Hu, B.Patel, Z.Zhou, S.Liang, R.Ybarra, Y.Qiu, G.Felsenfeld, J.Bungert, and S.Huang (2010).
H4R3 methylation facilitates beta-globin transcription by regulating histone acetyltransferase binding and H3 acetylation.
  Blood, 115, 2028-2037.  
20567261 Y.Yang, L.Hu, P.Wang, H.Hou, Y.Lin, Y.Liu, Z.Li, R.Gong, X.Feng, L.Zhou, W.Zhang, Y.Dong, H.Yang, H.Lin, Y.Wang, C.D.Chen, and Y.Xu (2010).
Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans.
  Cell Res, 20, 886-898.
PDB codes: 3n9l 3n9m 3n9n 3n9o 3n9p 3n9q
19541851 A.N.Scharf, T.K.Barth, and A.Imhof (2009).
Establishment of histone modifications after chromatin assembly.
  Nucleic Acids Res, 37, 5032-5040.  
19345099 A.Vasileva, D.Tiedau, A.Firooznia, T.Müller-Reichert, and R.Jessberger (2009).
Tdrd6 is required for spermiogenesis, chromatoid body architecture, and regulation of miRNA expression.
  Curr Biol, 19, 630-639.  
20048137 C.A.Musselman, and T.G.Kutateladze (2009).
PHD fingers: epigenetic effectors and potential drug targets.
  Mol Interv, 9, 314-323.  
19918066 C.Chen, J.Jin, D.A.James, M.A.Adams-Cioaba, J.G.Park, Y.Guo, E.Tenaglia, C.Xu, G.Gish, J.Min, and T.Pawson (2009).
Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi.
  Proc Natl Acad Sci U S A, 106, 20336-20341.
PDB code: 3fdr
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.  
19334741 G.Cui, M.V.Botuyan, and G.Mer (2009).
Preparation of recombinant peptides with site- and degree-specific lysine (13)C-methylation.
  Biochemistry, 48, 3798-3800.  
  20198186 J.Zheng, J.Lu, H.Liu, J.Li, and K.Chen (2009).
Sequence and structural analysis of 4SNc-Tudor domain protein from Takifugu Rubripes.
  Bioinformation, 4, 127-131.  
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.  
19273607 M.Pinskaya, A.Nair, D.Clynes, A.Morillon, and J.Mellor (2009).
Nucleosome remodeling and transcriptional repression are distinct functions of Isw1 in Saccharomyces cerevisiae.
  Mol Cell Biol, 29, 2419-2430.  
19184981 P.V.Peña, C.A.Musselman, A.J.Kuo, O.Gozani, and T.G.Kutateladze (2009).
NMR assignments and histone specificity of the ING2 PHD finger.
  Magn Reson Chem, 47, 352-358.  
19767730 R.Margueron, N.Justin, K.Ohno, M.L.Sharpe, J.Son, W.J.Drury, P.Voigt, S.R.Martin, W.R.Taylor, V.De Marco, V.Pirrotta, D.Reinberg, and S.J.Gamblin (2009).
Role of the polycomb protein EED in the propagation of repressive histone marks.
  Nature, 461, 762-767.
PDB codes: 3iiw 3iiy 3ij0 3ij1 3ijc
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
18718879 S.M.Fuchs, R.N.Laribee, and B.D.Strahl (2009).
Protein modifications in transcription elongation.
  Biochim Biophys Acta, 1789, 26-36.  
19684477 S.Pradhan, H.G.Chin, P.O.Estève, and S.E.Jacobsen (2009).
SET7/9 mediated methylation of non-histone proteins in mammalian cells.
  Epigenetics, 4, 383-387.  
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.  
19379692 T.Kim, and S.Buratowski (2009).
Dimethylation of H3K4 by Set1 recruits the Set3 histone deacetylase complex to 5' transcribed regions.
  Cell, 137, 259-272.  
19584108 V.V.Vagin, J.Wohlschlegel, J.Qu, Z.Jonsson, X.Huang, S.Chuma, A.Girard, R.Sachidanandam, G.J.Hannon, and A.A.Aravin (2009).
Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members.
  Genes Dev, 23, 1749-1762.  
19508735 X.Zhang, Y.V.Bernatavichute, S.Cokus, M.Pellegrini, and S.E.Jacobsen (2009).
Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana.
  Genome Biol, 10, R62.  
19233876 Y.Guo, N.Nady, C.Qi, A.Allali-Hassani, H.Zhu, P.Pan, M.A.Adams-Cioaba, M.F.Amaya, A.Dong, M.Vedadi, M.Schapira, R.J.Read, C.H.Arrowsmith, and J.Min (2009).
Methylation-state-specific recognition of histones by the MBT repeat protein L3MBTL2.
  Nucleic Acids Res, 37, 2204-2210.
PDB codes: 3cey 3f70
  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.  
18616348 A.L.Garske, G.Craciun, and J.M.Denu (2008).
A combinatorial H4 tail library for exploring the histone code.
  Biochemistry, 47, 8094-8102.  
18818090 C.Xu, G.Cui, M.V.Botuyan, and G.Mer (2008).
Structural basis for the recognition of methylated histone H3K36 by the Eaf3 subunit of histone deacetylase complex Rpd3S.
  Structure, 16, 1740-1750.
PDB codes: 2k3x 2k3y
18343668 F.Forneris, C.Binda, E.Battaglioli, and A.Mattevi (2008).
LSD1: oxidative chemistry for multifaceted functions in chromatin regulation.
  Trends Biochem Sci, 33, 181-189.  
18440794 F.Lan, A.C.Nottke, and Y.Shi (2008).
Mechanisms involved in the regulation of histone lysine demethylases.
  Curr Opin Cell Biol, 20, 316-325.  
18221488 G.Brosch, P.Loidl, and S.Graessle (2008).
Histone modifications and chromatin dynamics: a focus on filamentous fungi.
  FEMS Microbiol Rev, 32, 409-439.  
17668288 H.Tan, S.Wu, J.Wang, and Z.K.Zhao (2008).
The JMJD2 members of histone demethylase revisited.
  Mol Biol Rep, 35, 551-556.  
18562678 H.Yu, S.Zhu, B.Zhou, H.Xue, and J.D.Han (2008).
Inferring causal relationships among different histone modifications and gene expression.
  Genome Res, 18, 1314-1324.  
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.  
18084306 J.Lee, J.R.Thompson, M.V.Botuyan, and G.Mer (2008).
Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor.
  Nat Struct Mol Biol, 15, 109-111.
PDB codes: 2qqr 2qqs
18225984 K.A.Gelato, and W.Fischle (2008).
Role of histone modifications in defining chromatin structure and function.
  Biol Chem, 389, 353-363.  
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
18728284 M.Y.Wu, K.W.Eldin, and A.L.Beaudet (2008).
Identification of chromatin remodeling genes Arid4a and Arid4b as leukemia suppressor genes.
  J Natl Cancer Inst, 100, 1247-1259.  
18408754 N.Kalakonda, W.Fischle, P.Boccuni, N.Gurvich, R.Hoya-Arias, X.Zhao, Y.Miyata, D.Macgrogan, J.Zhang, J.K.Sims, J.C.Rice, and S.D.Nimer (2008).
Histone H4 lysine 20 monomethylation promotes transcriptional repression by L3MBTL1.
  Oncogene, 27, 4293-4304.  
18451103 P.A.Cloos, J.Christensen, K.Agger, and K.Helin (2008).
Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease.
  Genes Dev, 22, 1115-1140.  
18564434 P.Hahn, J.Böse, S.Edler, and A.Lengeling (2008).
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.
  BMC Genomics, 9, 293.  
18086877 R.Cao, H.Wang, J.He, H.Erdjument-Bromage, P.Tempst, and Y.Zhang (2008).
Role of hPHF1 in H3K27 methylation and Hox gene silencing.
  Mol Cell Biol, 28, 1862-1872.  
17218268 A.J.Ruthenburg, C.D.Allis, and J.Wysocka (2007).
Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark.
  Mol Cell, 25, 15-30.  
18037899 A.J.Ruthenburg, H.Li, D.J.Patel, and C.D.Allis (2007).
Multivalent engagement of chromatin modifications by linked binding modules.
  Nat Rev Mol Cell Biol, 8, 983-994.  
17471263 A.Wolf, C.Schmitz, and A.Böttger (2007).
Changing story of the receptor for phosphatidylserine-dependent clearance of apoptotic cells.
  EMBO Rep, 8, 465-469.  
17151105 B.Alberter, and A.Ensser (2007).
Histone modification pattern of the T-cellular Herpesvirus saimiri genome in latency.
  J Virol, 81, 2524-2530.  
17932512 C.Grimm, A.G.de Ayala Alonso, V.Rybin, U.Steuerwald, N.Ly-Hartig, W.Fischle, J.Müller, and C.W.Müller (2007).
Structural and functional analyses of methyl-lysine binding by the malignant brain tumour repeat protein Sex comb on midleg.
  EMBO Rep, 8, 1031-1037.
PDB codes: 2r57 2r58 2r5a 2r5m
17687328 F.Lan, R.E.Collins, R.De Cegli, R.Alpatov, J.R.Horton, X.Shi, O.Gozani, X.Cheng, and Y.Shi (2007).
Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression.
  Nature, 448, 718-722.
PDB code: 2puy
17988933 G.Kustatscher, and A.G.Ladurner (2007).
Modular paths to 'decoding' and 'wiping' histone lysine methylation.
  Curr Opin Chem Biol, 11, 628-635.  
18042461 H.Li, W.Fischle, W.Wang, E.M.Duncan, L.Liang, S.Murakami-Ishibe, C.D.Allis, and D.J.Patel (2007).
Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger.
  Mol Cell, 28, 677-691.
PDB codes: 2rhi 2rhu 2rhx 2rhy 2rhz 2ri2 2ri3 2ri5 2ri7
17589523 J.F.Couture, E.Collazo, P.A.Ortiz-Tello, J.S.Brunzelle, and R.C.Trievel (2007).
Specificity and mechanism of JMJD2A, a trimethyllysine-specific histone demethylase.
  Nat Struct Mol Biol, 14, 689-695.
PDB codes: 2q8c 2q8d 2q8e
18026117 J.Min, A.Allali-Hassani, N.Nady, C.Qi, H.Ouyang, Y.Liu, F.MacKenzie, M.Vedadi, and C.H.Arrowsmith (2007).
L3MBTL1 recognition of mono- and dimethylated histones.
  Nat Struct Mol Biol, 14, 1229-1230.
PDB codes: 2pqw 2rjc 2rjd 2rje 2rjf
17277801 L.Corsini, and M.Sattler (2007).
Tudor hooks up with DNA repair.
  Nat Struct Mol Biol, 14, 98-99.  
17949986 M.A.Soliman, and K.Riabowol (2007).
After a decade of study-ING, a PHD for a versatile family of proteins.
  Trends Biochem Sci, 32, 509-519.  
17632523 N.Shaw, M.Zhao, C.Cheng, H.Xu, J.Saarikettu, Y.Li, Y.Da, Z.Yao, O.Silvennoinen, J.Yang, Z.J.Liu, B.C.Wang, and Z.Rao (2007).
The multifunctional human p100 protein 'hooks' methylated ligands.
  Nat Struct Mol Biol, 14, 779-784.  
17694085 P.Karagianni, and J.Wong (2007).
HDAC3: taking the SMRT-N-CoRrect road to repression.
  Oncogene, 26, 5439-5449.  
17504018 P.Stavropoulos, and A.Hoelz (2007).
Lysine-specific demethylase 1 as a potential therapeutic target.
  Expert Opin Ther Targets, 11, 809-820.  
17540172 P.Trojer, G.Li, R.J.Sims, A.Vaquero, N.Kalakonda, P.Boccuni, D.Lee, H.Erdjument-Bromage, P.Tempst, S.D.Nimer, Y.H.Wang, and D.Reinberg (2007).
L3MBTL1, a histone-methylation-dependent chromatin lock.
  Cell, 129, 915-928.  
17715366 R.A.Howard-Till, and M.C.Yao (2007).
Tudor nuclease genes and programmed DNA rearrangements in Tetrahymena thermophila.
  Eukaryot Cell, 6, 1795-1804.  
17342184 R.J.Klose, and Y.Zhang (2007).
Regulation of histone methylation by demethylimination and demethylation.
  Nat Rev Mol Cell Biol, 8, 307-318.  
17984969 R.J.Klose, and Y.Zhang (2007).
Histone H3 Arg2 methylation provides alternative directions for COMPASS.
  Nat Struct Mol Biol, 14, 1058-1060.  
18074396 R.L.Rich, and D.G.Myszka (2007).
Survey of the year 2006 commercial optical biosensor literature.
  J Mol Recognit, 20, 300-366.  
17984965 S.D.Taverna, H.Li, A.J.Ruthenburg, C.D.Allis, and D.J.Patel (2007).
How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers.
  Nat Struct Mol Biol, 14, 1025-1040.  
17522673 S.L.Berger (2007).
The complex language of chromatin regulation during transcription.
  Nature, 447, 407-412.  
17984971 S.Lall (2007).
Primers on chromatin.
  Nat Struct Mol Biol, 14, 1110-1115.  
18025461 S.Ramón-Maiques, A.J.Kuo, D.Carney, A.G.Matthews, M.A.Oettinger, O.Gozani, and W.Yang (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.
PDB codes: 2v83 2v85 2v86 2v87 2v88
17266133 S.Wang, F.He, W.Xiong, S.Gu, H.Liu, T.Zhang, X.Yu, and Y.Chen (2007).
Polycomblike-2-deficient mice exhibit normal left-right asymmetry.
  Dev Dyn, 236, 853-861.  
17320507 T.Kouzarides (2007).
Chromatin modifications and their function.
  Cell, 128, 693-705.  
17277881 X.Tian, and J.Fang (2007).
Current perspectives on histone demethylases.
  Acta Biochim Biophys Sin (Shanghai), 39, 81-88.  
17567753 Z.Chen, J.Zang, J.Kappler, X.Hong, F.Crawford, Q.Wang, F.Lan, C.Jiang, J.Whetstine, S.Dai, K.Hansen, Y.Shi, and G.Zhang (2007).
Structural basis of the recognition of a methylated histone tail by JMJD2A.
  Proc Natl Acad Sci U S A, 104, 10818-10823.
PDB codes: 2p5b 2pxj
16829959 A.J.Ruthenburg, W.Wang, D.M.Graybosch, H.Li, C.D.Allis, D.J.Patel, and G.L.Verdine (2006).
Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex.
  Nat Struct Mol Biol, 13, 704-712.
PDB codes: 2cnx 2co0 2h68 2h6k 2h6n 2h6q
16946699 A.Schuetz, A.Allali-Hassani, F.Martín, P.Loppnau, M.Vedadi, A.Bochkarev, A.N.Plotnikov, C.H.Arrowsmith, and J.Min (2006).
Structural basis for molecular recognition and presentation of histone H3 by WDR5.
  EMBO J, 25, 4245-4252.
PDB codes: 2gnq 2h9l 2h9m 2h9n 2h9o 2h9p 2o9k
16829979 B.T.Seet, I.Dikic, M.M.Zhou, and T.Pawson (2006).
Reading protein modifications with interaction domains.
  Nat Rev Mol Cell Biol, 7, 473-483.  
16923967 D.G.Martin, K.Baetz, X.Shi, K.L.Walter, V.E.MacDonald, M.J.Wlodarski, O.Gozani, P.Hieter, and L.Howe (2006).
The Yng1p plant homeodomain finger is a methyl-histone binding module that recognizes lysine 4-methylated histone H3.
  Mol Cell Biol, 26, 7871-7879.  
16829960 J.F.Couture, E.Collazo, and R.C.Trievel (2006).
Molecular recognition of histone H3 by the WD40 protein WDR5.
  Nat Struct Mol Biol, 13, 698-703.
PDB codes: 2h13 2h14
17070031 J.F.Couture, and R.C.Trievel (2006).
Histone-modifying enzymes: encrypting an enigmatic epigenetic code.
  Curr Opin Struct Biol, 16, 753-760.  
16839870 J.Mellor (2006).
It takes a PHD to read the histone code.
  Cell, 126, 22-24.  
16843890 M.S.Cosgrove (2006).
PHinDing a new histone "effector" domain.
  Structure, 14, 1096-1098.  
17190600 M.V.Botuyan, J.Lee, I.M.Ward, J.E.Kim, J.R.Thompson, J.Chen, and G.Mer (2006).
Structural basis for the methylation state-specific recognition of histone H4-K20 by 53BP1 and Crb2 in DNA repair.
  Cell, 127, 1361-1373.
PDB codes: 2fhd 2g3r 2ig0
16823438 P.B.Becker (2006).
Gene regulation: a finger on the mark.
  Nature, 442, 31-32.  
16983801 R.J.Klose, E.M.Kallin, and Y.Zhang (2006).
JmjC-domain-containing proteins and histone demethylation.
  Nat Rev Genet, 7, 715-727.  
16732292 R.J.Klose, K.Yamane, Y.Bae, D.Zhang, H.Erdjument-Bromage, P.Tempst, J.Wong, and Y.Zhang (2006).
The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36.
  Nature, 442, 312-316.  
16826231 Y.Zhang (2006).
It takes a PHD to interpret histone methylation.
  Nat Struct Mol Biol, 13, 572-574.  
16677698 Z.Chen, J.Zang, J.Whetstine, X.Hong, F.Davrazou, T.G.Kutateladze, M.Simpson, Q.Mao, C.H.Pan, S.Dai, J.Hagman, K.Hansen, Y.Shi, and G.Zhang (2006).
Structural insights into histone demethylation by JMJD2 family members.
  Cell, 125, 691-702.
PDB codes: 2gp3 2gp5
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 code is shown on the right.

 

spacer
spacer