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PDBsum entry 2puy

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protein ligands metals Protein-protein interface(s) links
Transcription PDB id
2puy
Jmol
Contents
Protein chains
59 a.a. *
60 a.a. *
Ligands
ALA-ARG-THR-LYS-
GLN-THR-ALA-ARG-
LYS-SER
Metals
_ZN ×4
Waters ×88
* Residue conservation analysis
PDB id:
2puy
Name: Transcription
Title: Crystal structure of the bhc80 phd finger
Structure: Phd finger protein 21a. Chain: a, b. Fragment: phd finger residues: 486-543. Synonym: braf35-hdac complex protein bhc80, bhc80a. Engineered: yes. Histone h3. Chain: e. Fragment: h3 1-10. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: phf21a, bhc80, kiaa1696. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Other_details: synthesized peptide
Resolution:
1.43Å     R-factor:   0.206     R-free:   0.231
Authors: J.R.Horton,X.Cheng,R.E.Collins
Key ref:
F.Lan et al. (2007). Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature, 448, 718-722. PubMed id: 17687328 DOI: 10.1038/nature06034
Date:
09-May-07     Release date:   14-Aug-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q96BD5  (PF21A_HUMAN) -  PHD finger protein 21A
Seq:
Struc:
 
Seq:
Struc:
680 a.a.
59 a.a.*
Protein chain
Pfam   ArchSchema ?
Q96BD5  (PF21A_HUMAN) -  PHD finger protein 21A
Seq:
Struc:
 
Seq:
Struc:
680 a.a.
60 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     zinc ion binding     1 term  

 

 
DOI no: 10.1038/nature06034 Nature 448:718-722 (2007)
PubMed id: 17687328  
 
 
Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression.
F.Lan, R.E.Collins, R.De Cegli, R.Alpatov, J.R.Horton, X.Shi, O.Gozani, X.Cheng, Y.Shi.
 
  ABSTRACT  
 
Histone methylation is crucial for regulating chromatin structure, gene transcription and the epigenetic state of the cell. LSD1 is a lysine-specific histone demethylase that represses transcription by demethylating histone H3 on lysine 4 (ref. 1). The LSD1 complex contains a number of proteins, all of which have been assigned roles in events upstream of LSD1-mediated demethylation apart from BHC80 (also known as PHF21A), a plant homeodomain (PHD) finger-containing protein. Here we report that, in contrast to the PHD fingers of the bromodomain PHD finger transcription factor (BPTF) and inhibitor of growth family 2 (ING2), which bind methylated H3K4 (H3K4me3), the PHD finger of BHC80 binds unmethylated H3K4 (H3K4me0), and this interaction is specifically abrogated by methylation of H3K4. The crystal structure of the PHD finger of BHC80 bound to an unmodified H3 peptide has revealed the structural basis of the recognition of H3K4me0. Knockdown of BHC80 by RNA inhibition results in the de-repression of LSD1 target genes, and this repression is restored by the reintroduction of wild-type BHC80 but not by a PHD-finger mutant that cannot bind H3. Chromatin immunoprecipitation showed that BHC80 and LSD1 depend reciprocally on one another to associate with chromatin. These findings couple the function of BHC80 to that of LSD1, and indicate that unmodified H3K4 is part of the 'histone code'. They further raise the possibility that the generation and recognition of the unmodified state on histone tails in general might be just as crucial as post-translational modifications of histone for chromatin and transcriptional regulation.
 
  Selected figure(s)  
 
Figure 2.
Figure 2: Structure of BHC80 PHD with H3 1–10. a, Cross-brace topology of the PHD domain. Residues involved in peptide binding are underlined. Bold residues are those involved in chelating Zn. b, The H3 peptide binds BHC80 as an anti-parallel -strand (grey). c, Peptide binding is specified by the insertion of M502 between H3R2 and H3K4 and D489 between H3K4 and H3R8. D489 and E488 bind H3K4, and H487 (4.0 Å away) restricts methyl-lysine binding (Supplementary Fig. 4). The N-terminal amine of H3 is caged by carbonyl oxygens, and H3A1 is recognized by a shallow hydrophobic pocket. d, Mutation of D489 and M502 disrupt PHD binding to unmodified H3. WT, wild type.
Figure 3.
Figure 3: Structural comparison of PHD fingers. a, Superimposition of PHD domains of BHC80 (PDB 2PUY, green, H3 grey), BPTF (PDB 2F6J, red, H3 pink) and ING2 (PDB 2GQ6, blue, H3 purple). b, Recognition of H3K4 by BHC80 (left) and binding of H3K4me3 by BPTF (middle) and ING2 (right); colours as in a. c, Sequence alignment of the PHD fingers of BHC80, BPTF and ING2. Zinc-binding residues are bold, K4-binding residues blue and the R2-binding pocket, red. Residues that form the N-amine and A1 binding pockets are green. Residues that form the anti-parallel -sheet with peptide are underlined. Stars mark invariant residues, and colons denote conservation.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2007, 448, 718-722) copyright 2007.  
  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).
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Suppression of the antiviral response by an influenza histone mimic.
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20803232 A.H.Aguissa-Touré, R.P.Wong, and G.Li (2011).
The ING family tumor suppressors: from structure to function.
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21483810 B.Guillemette, P.Drogaris, H.H.Lin, H.Armstrong, K.Hiragami-Hamada, A.Imhof, E.Bonneil, P.Thibault, A.Verreault, and R.J.Festenstein (2011).
H3 lysine 4 is acetylated at active gene promoters and is regulated by H3 lysine 4 methylation.
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21423274 M.Yun, J.Wu, J.L.Workman, and B.Li (2011).
Readers of histone modifications.
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21059680 P.Slama, and D.Geman (2011).
Identification of family-determining residues in PHD fingers.
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21419134 Y.Chang, J.R.Horton, M.T.Bedford, X.Zhang, and X.Cheng (2011).
Structural insights for MPP8 chromodomain interaction with histone H3 lysine 9: potential effect of phosphorylation on methyl-lysine binding.
  J Mol Biol, 408, 807-814.
PDB code: 3qo2
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Combinatorial profiling of chromatin binding modules reveals multisite discrimination.
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20615959 A.S.Koh, R.E.Kingston, C.Benoist, and D.Mathis (2010).
Global relevance of Aire binding to hypomethylated lysine-4 of histone-3.
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20192747 C.Liu, F.Lu, X.Cui, and X.Cao (2010).
Histone methylation in higher plants.
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20566703 C.Steilmann, M.C.Cavalcanti, M.Bergmann, S.Kliesch, W.Weidner, and K.Steger (2010).
Aberrant mRNA expression of chromatin remodelling factors in round spermatid maturation arrest compared with normal human spermatogenesis.
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20713442 C.T.Foster, O.M.Dovey, L.Lezina, J.L.Luo, T.W.Gant, N.Barlev, A.Bradley, and S.M.Cowley (2010).
Lysine-specific demethylase 1 regulates the embryonic transcriptome and CoREST stability.
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Structural insight into the zinc finger CW domain as a histone modification reader.
  Structure, 18, 1127-1139.
PDB codes: 2e61 2rr4
  21339843 H.Hashimoto, P.M.Vertino, and X.Cheng (2010).
Molecular coupling of DNA methylation and histone methylation.
  Epigenomics, 2, 657-669.  
20567262 H.Lin, Y.Wang, Y.Wang, F.Tian, P.Pu, Y.Yu, H.Mao, Y.Yang, P.Wang, L.Hu, Y.Lin, Y.Liu, Y.Xu, and C.D.Chen (2010).
Coordinated regulation of active and repressive histone methylations by a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans.
  Cell Res, 20, 899-907.  
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
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.  
20101266 L.Yu, Y.Wang, S.Huang, J.Wang, Z.Deng, Q.Zhang, W.Wu, X.Zhang, Z.Liu, W.Gong, and Z.Chen (2010).
Structural insights into a novel histone demethylase PHF8.
  Cell Res, 20, 166-173.
PDB codes: 3k3n 3k3o
  20574068 M.D.Taylor, S.Sadhukhan, P.Kottangada, A.Ramgopal, K.Sarkar, S.D'Silva, A.Selvakumar, F.Candotti, and Y.M.Vyas (2010).
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  PLoS One, 5, e15541.  
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Reversal of histone methylation: biochemical and molecular mechanisms of histone demethylases.
  Annu Rev Biochem, 79, 155-179.  
20126658 Q.Zhang, S.Chakravarty, D.Ghersi, L.Zeng, A.N.Plotnikov, R.Sanchez, and M.M.Zhou (2010).
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  Biochemistry, 49, 6576-6586.
PDB codes: 2kyu 2kyx
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TRIM24 links a non-canonical histone signature to breast cancer.
  Nature, 468, 927-932.
PDB codes: 3o33 3o34 3o35 3o36 3o37
20210320 X.Cheng, and R.M.Blumenthal (2010).
Coordinated chromatin control: structural and functional linkage of DNA and histone methylation.
  Biochemistry, 49, 2999-3008.  
20631708 Y.Jacob, H.Stroud, C.Leblanc, S.Feng, L.Zhuo, E.Caro, C.Hassel, C.Gutierrez, S.D.Michaels, and S.E.Jacobsen (2010).
Regulation of heterochromatic DNA replication by histone H3 lysine 27 methyltransferases.
  Nature, 466, 987-991.  
20379134 Y.Tanaka, K.Okamoto, K.Teye, T.Umata, N.Yamagiwa, Y.Suto, Y.Zhang, and M.Tsuneoka (2010).
JmjC enzyme KDM2A is a regulator of rRNA transcription in response to starvation.
  EMBO J, 29, 1510-1522.  
18780289 A.H.Coles, and S.N.Jones (2009).
The ING gene family in the regulation of cell growth and tumorigenesis.
  J Cell Physiol, 218, 45-57.  
19522008 B.Laurent, V.Randrianarison-Huetz, Z.Kadri, P.H.Roméo, F.Porteu, and D.Duménil (2009).
Gfi-1B promoter remains associated with active chromatin marks throughout erythroid differentiation of human primary progenitor cells.
  Stem Cells, 27, 2153-2162.  
19155214 B.Li, J.Jackson, M.D.Simon, B.Fleharty, M.Gogol, C.Seidel, J.L.Workman, and A.Shilatifard (2009).
Histone H3 Lysine 36 Dimethylation (H3K36me2) Is Sufficient to Recruit the Rpd3s Histone Deacetylase Complex and to Repress Spurious Transcription.
  J Biol Chem, 284, 7970-7976.  
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.  
19575660 D.H.Kim, M.R.Doyle, S.Sung, and R.M.Amasino (2009).
Vernalization: winter and the timing of flowering in plants.
  Annu Rev Cell Dev Biol, 25, 277-299.  
19302042 D.Mathis, and C.Benoist (2009).
Aire.
  Annu Rev Immunol, 27, 287-312.  
19337993 D.W.Chan, Y.Wang, M.Wu, J.Wong, J.Qin, and Y.Zhao (2009).
Unbiased proteomic screen for binding proteins to modified lysines on histone H3.
  Proteomics, 9, 2343-2354.  
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
19381457 F.Lan, and Y.Shi (2009).
Epigenetic regulation: methylation of histone and non-histone proteins.
  Sci China C Life Sci, 52, 311-322.  
19382993 G.A.Holländer, and P.Peterson (2009).
Learning to be tolerant: how T cells keep out of trouble.
  J Intern Med, 265, 541-561.  
19430464 G.G.Wang, J.Song, Z.Wang, H.L.Dormann, F.Casadio, H.Li, J.L.Luo, D.J.Patel, and C.D.Allis (2009).
Haematopoietic malignancies caused by dysregulation of a chromatin-binding PHD finger.
  Nature, 459, 847-851.
PDB codes: 2kgg 2kgi 3gl6
19394292 J.Ouyang, Y.Shi, A.Valin, Y.Xuan, and G.Gill (2009).
Direct binding of CoREST1 to SUMO-2/3 contributes to gene-specific repression by the LSD1/CoREST1/HDAC complex.
  Mol Cell, 34, 145-154.  
19221587 K.Chen, and L.Kurgan (2009).
Investigation of atomic level patterns in protein--small ligand interactions.
  PLoS ONE, 4, e4473.  
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.  
19364764 Q.Fu, X.Yu, C.W.Callaway, R.H.Lane, and R.A.McKnight (2009).
Epigenetics: intrauterine growth retardation (IUGR) modifies the histone code along the rat hepatic IGF-1 gene.
  FASEB J, 23, 2438-2449.  
18831036 R.Suzuki, H.Shindo, A.Tase, Y.Kikuchi, M.Shimizu, and T.Yamazaki (2009).
Solution structures and DNA binding properties of the N-terminal SAP domains of SUMO E3 ligases from Saccharomyces cerevisiae and Oryza sativa.
  Proteins, 75, 336-347.
PDB codes: 2rnn 2rno
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.  
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.  
19434754 T.Gao, R.E.Collins, J.R.Horton, X.Zhang, R.Zhang, A.Dhayalan, R.Tamas, A.Jeltsch, and X.Cheng (2009).
The ankyrin repeat domain of Huntingtin interacting protein 14 contains a surface aromatic cage, a potential site for methyl-lysine binding.
  Proteins, 76, 772-777.
PDB code: 3eu9
19154204 W.Y.Lee, D.Lee, W.I.Chung, and C.S.Kwon (2009).
Arabidopsis ING and Alfin1-like protein families localize to the nucleus and bind to H3K4me3/2 via plant homeodomain fingers.
  Plant J, 58, 511-524.  
19481593 Y.J.Cui, R.L.Yeager, X.B.Zhong, and C.D.Klaassen (2009).
Ontogenic expression of hepatic Ahr mRNA is associated with histone H3K4 di-methylation during mouse liver development.
  Toxicol Lett, 189, 184-190.  
19073934 A.Grishok, S.Hoersch, and P.A.Sharp (2008).
RNA interference and retinoblastoma-related genes are required for repression of endogenous siRNA targets in Caenorhabditis elegans.
  Proc Natl Acad Sci U S A, 105, 20386-20391.  
18840680 A.S.Koh, A.J.Kuo, S.Y.Park, P.Cheung, J.Abramson, D.Bua, D.Carney, S.E.Shoelson, O.Gozani, R.E.Kingston, C.Benoist, and D.Mathis (2008).
Aire employs a histone-binding module to mediate immunological tolerance, linking chromatin regulation with organ-specific autoimmunity.
  Proc Natl Acad Sci U S A, 105, 15878-15883.  
18425769 D.R.Walkinshaw, S.Tahmasebi, N.R.Bertos, and X.J.Yang (2008).
Histone deacetylases as transducers and targets of nuclear signaling.
  J Cell Biochem, 104, 1541-1552.  
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.  
19011376 G.Musco, and P.Peterson (2008).
PHD finger of autoimmune regulator: An epigenetic link between the histone modifications and tissue-specific antigen expression in thymus.
  Epigenetics, 3, 310-314.  
18772888 H.Hashimoto, J.R.Horton, X.Zhang, M.Bostick, S.E.Jacobsen, and X.Cheng (2008).
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
  Nature, 455, 826-829.
PDB codes: 2zo0 2zo1 2zo2
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.  
18319736 M.M.Brent, and R.Marmorstein (2008).
Ankyrin for methylated lysines.
  Nat Struct Mol Biol, 15, 221-222.  
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.  
18533182 P.V.Peña, R.A.Hom, T.Hung, H.Lin, A.J.Kuo, R.P.Wong, O.M.Subach, K.S.Champagne, R.Zhao, V.V.Verkhusha, G.Li, O.Gozani, and T.G.Kutateladze (2008).
Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor.
  J Mol Biol, 380, 303-312.
PDB code: 2qic
18264113 R.E.Collins, J.P.Northrop, J.R.Horton, D.Y.Lee, X.Zhang, M.R.Stallcup, and X.Cheng (2008).
The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules.
  Nat Struct Mol Biol, 15, 245-250.
PDB codes: 3b7b 3b95
18784729 R.J.Sims, and D.Reinberg (2008).
Is there a code embedded in proteins that is based on post-translational modifications?
  Nat Rev Mol Cell Biol, 9, 815-820.  
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The PHD domain of Np95 (mUHRF1) is involved in large-scale reorganization of pericentromeric heterochromatin.
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