Structure and site-specific recognition of histone H3 by the PHD finger of human autoimmune regulator.

PubWeight™: 1.35‹?› | Rank: Top 10%

🔗 View Article (PMC 2923636)

Published in Structure on May 13, 2009

Authors

Suvobrata Chakravarty1, Lei Zeng, Ming-Ming Zhou

Author Affiliations

1: Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, One Gustave L Levy Place, New York, NY 10029, USA.

Articles citing this

Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature (2010) 2.02

The PHD finger: a versatile epigenome reader. Trends Biochem Sci (2011) 1.81

Handpicking epigenetic marks with PHD fingers. Nucleic Acids Res (2011) 1.69

Plant homeodomain (PHD) fingers of CHD4 are histone H3-binding modules with preference for unmodified H3K4 and methylated H3K9. J Biol Chem (2011) 1.55

Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia. Genome Res (2014) 1.38

Aire and T cell development. Curr Opin Immunol (2010) 1.36

Keeping it in the family: diverse histone recognition by conserved structural folds. Crit Rev Biochem Mol Biol (2010) 1.29

PHD fingers: epigenetic effectors and potential drug targets. Mol Interv (2009) 1.21

Global relevance of Aire binding to hypomethylated lysine-4 of histone-3. Proc Natl Acad Sci U S A (2010) 1.17

AIRE in the thymus and beyond. Curr Opin Immunol (2009) 1.16

The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications. Cell Cycle (2012) 1.14

Structural basis for site-specific reading of unmodified R2 of histone H3 tail by UHRF1 PHD finger. Cell Res (2011) 1.02

The CW domain, a new histone recognition module in chromatin proteins. EMBO J (2011) 1.01

Exploring PHD fingers and H3K4me0 interactions with molecular dynamics simulations and binding free energy calculations: AIRE-PHD1, a comparative study. PLoS One (2012) 0.96

AIRE-PHD fingers are structural hubs to maintain the integrity of chromatin-associated interactome. Nucleic Acids Res (2012) 0.95

The PHD finger of human UHRF1 reveals a new subgroup of unmethylated histone H3 tail readers. PLoS One (2011) 0.92

The role of Aire in clonal selection. Immunol Cell Biol (2010) 0.90

Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism. Nat Commun (2015) 0.90

The PHD1 finger of KDM5B recognizes unmodified H3K4 during the demethylation of histone H3K4me2/3 by KDM5B. Protein Cell (2014) 0.89

Solution NMR structure and histone binding of the PHD domain of human MLL5. PLoS One (2013) 0.88

ChIP-less analysis of chromatin states. Epigenetics Chromatin (2014) 0.87

Aire's plant homeodomain(PHD)-2 is critical for induction of immunological tolerance. Proc Natl Acad Sci U S A (2013) 0.84

Sequence requirements for combinatorial recognition of histone H3 by the MRG15 and Pf1 subunits of the Rpd3S/Sin3S corepressor complex. J Mol Biol (2012) 0.84

Human APECED; a Sick Thymus Syndrome? Front Immunol (2013) 0.82

Models of aire-dependent gene regulation for thymic negative selection. Front Immunol (2011) 0.80

Protein and DNA modifications: evolutionary imprints of bacterial biochemical diversification and geochemistry on the provenance of eukaryotic epigenetics. Cold Spring Harb Perspect Biol (2014) 0.77

Central tolerance to self revealed by the autoimmune regulator. Ann N Y Acad Sci (2015) 0.76

Partners in crime: The role of tandem modules in gene transcription. Protein Sci (2015) 0.76

Autoimmune Regulator (AIRE) Is Expressed in Spermatogenic Cells, and It Altered the Expression of Several Nucleic-Acid-Binding and Cytoskeletal Proteins in Germ Cell 1 Spermatogonial (GC1-spg) Cells. Mol Cell Proteomics (2016) 0.75

Articles cited by this

MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89

Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol (1993) 64.61

AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR (1996) 29.55

Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng (1998) 28.09

Projection of an immunological self shadow within the thymus by the aire protein. Science (2002) 12.15

Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res (1999) 11.64

Hidden Markov models. Curr Opin Struct Biol (1996) 11.56

DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature (2007) 11.14

Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol Cell (2007) 9.73

Structure and function of a human TAFII250 double bromodomain module. Science (2000) 8.00

Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature (2006) 7.70

Molecular mechanism of histone H3K4me3 recognition by plant homeodomain of ING2. Nature (2006) 7.52

Promiscuous gene expression in medullary thymic epithelial cells mirrors the peripheral self. Nat Immunol (2001) 7.30

The PHD finger: implications for chromatin-mediated transcriptional regulation. Trends Biochem Sci (1995) 6.97

Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell (2007) 6.62

Regulation of HP1-chromatin binding by histone H3 methylation and phosphorylation. Nature (2005) 6.40

Aire regulates negative selection of organ-specific T cells. Nat Immunol (2003) 5.85

Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature (2005) 5.53

Positional cloning of the APECED gene. Nat Genet (1997) 5.47

Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science (2006) 4.54

Recognition of unmethylated histone H3 lysine 4 links BHC80 to LSD1-mediated gene repression. Nature (2007) 4.49

Promiscuous gene expression in thymic epithelial cells is regulated at multiple levels. J Exp Med (2005) 4.06

Organismal differences in post-translational modifications in histones H3 and H4. J Biol Chem (2006) 3.84

Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive. Nature (2007) 3.68

Multidimensional heteronuclear nuclear magnetic resonance of proteins. Methods Enzymol (1994) 3.45

Aire deficient mice develop multiple features of APECED phenotype and show altered immune response. Hum Mol Genet (2002) 2.91

Solution structure of the PHD domain from the KAP-1 corepressor: structural determinants for PHD, RING and LIM zinc-binding domains. EMBO J (2001) 2.54

The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2. Proc Natl Acad Sci U S A (2007) 2.53

The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression. EMBO Rep (2008) 2.22

Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex. Mol Cell (2008) 2.09

Transcriptional regulation by AIRE: molecular mechanisms of central tolerance. Nat Rev Immunol (2008) 1.99

Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. Genes Dev (2008) 1.96

Autoregulation of the rsc4 tandem bromodomain by gcn5 acetylation. Mol Cell (2007) 1.85

Aire employs a histone-binding module to mediate immunological tolerance, linking chromatin regulation with organ-specific autoimmunity. Proc Natl Acad Sci U S A (2008) 1.83

Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3. Structure (2008) 1.72

Treble clef finger--a functionally diverse zinc-binding structural motif. Nucleic Acids Res (2001) 1.71

Pancreatic gene expression in rare cells of thymic medulla: evidence for functional contribution to T cell tolerance. Int Immunol (1997) 1.50

Comparative genomics and structural biology of the molecular innovations of eukaryotes. Curr Opin Struct Biol (2006) 1.36

Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing. Nat Struct Mol Biol (2008) 1.32

Provenance of SET-domain histone methyltransferases through duplication of a simple structural unit. Cell Cycle (2003) 0.96

Crystal structure analysis of the PHD domain of the transcription co-activator Pygopus. J Mol Biol (2007) 0.95

Role of PHD fingers and COOH-terminal 30 amino acids in AIRE transactivation activity. Mol Immunol (2007) 0.90

Death in the AIRE. Trends Immunol (2008) 0.79

Articles by these authors

Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell (2010) 6.94

Structure and conserved RNA binding of the PAZ domain. Nature (2003) 5.28

Reading protein modifications with interaction domains. Nat Rev Mol Cell Biol (2006) 4.55

Brd4 coactivates transcriptional activation of NF-kappaB via specific binding to acetylated RelA. Mol Cell Biol (2008) 3.74

Methylation of a histone mimic within the histone methyltransferase G9a regulates protein complex assembly. Mol Cell (2007) 3.51

Histone demethylase JMJD3 contributes to epigenetic control of INK4a/ARF by oncogenic RAS. Genes Dev (2009) 2.98

PHD domain-mediated E3 ligase activity directs intramolecular sumoylation of an adjacent bromodomain required for gene silencing. Mol Cell (2007) 2.77

The MMSET protein is a histone methyltransferase with characteristics of a transcriptional corepressor. Blood (2007) 2.58

Structural mechanism of the bromodomain of the coactivator CBP in p53 transcriptional activation. Mol Cell (2004) 2.43

Structure and regulation of MAPK phosphatases. Cell Signal (2004) 2.42

Structural basis of lysine-acetylated HIV-1 Tat recognition by PCAF bromodomain. Mol Cell (2002) 2.20

Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature (2010) 2.02

The role of human bromodomains in chromatin biology and gene transcription. Curr Opin Drug Discov Devel (2009) 1.99

BET bromodomain-targeting compounds reactivate HIV from latency via a Tat-independent mechanism. Cell Cycle (2012) 1.88

Structural basis of site-specific histone recognition by the bromodomains of human coactivators PCAF and CBP/p300. Structure (2008) 1.86

The PHD finger: a versatile epigenome reader. Trends Biochem Sci (2011) 1.81

A dimeric viral SET domain methyltransferase specific to Lys27 of histone H3. Nat Struct Biol (2003) 1.67

Down-regulation of NF-κB transcriptional activity in HIV-associated kidney disease by BRD4 inhibition. J Biol Chem (2012) 1.66

Solution structure of the MAPK phosphatase PAC-1 catalytic domain. Insights into substrate-induced enzymatic activation of MKP. Structure (2003) 1.54

Transcriptional synergy between Tat and PCAF is dependent on the binding of acetylated Tat to the PCAF bromodomain. EMBO J (2002) 1.49

BRD4 sustains melanoma proliferation and represents a new target for epigenetic therapy. Cancer Res (2013) 1.43

Two-pronged binding with bromodomain-containing protein 4 liberates positive transcription elongation factor b from inactive ribonucleoprotein complexes. J Biol Chem (2011) 1.43

A small molecule binding to the coactivator CREB-binding protein blocks apoptosis in cardiomyocytes. Chem Biol (2011) 1.35

Epigenetic transcriptional repression of cellular genes by a viral SET protein. Nat Cell Biol (2008) 1.34

Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing. Nat Struct Mol Biol (2008) 1.32

Long noncoding RNA, polycomb, and the ghosts haunting INK4b-ARF-INK4a expression. Cancer Res (2011) 1.31

Structural insights of the specificity and catalysis of a viral histone H3 lysine 27 methyltransferase. J Mol Biol (2006) 1.30

Keeping it in the family: diverse histone recognition by conserved structural folds. Crit Rev Biochem Mol Biol (2010) 1.29

Structure and hemimethylated CpG binding of the SRA domain from human UHRF1. J Biol Chem (2008) 1.26

Target structure-based discovery of small molecules that block human p53 and CREB binding protein association. Chem Biol (2006) 1.25

Selective small molecules blocking HIV-1 Tat and coactivator PCAF association. J Am Chem Soc (2005) 1.18

p53-induced growth arrest is regulated by the mitochondrial SirT3 deacetylase. PLoS One (2010) 1.18

Structure and mechanisms of lysine methylation recognition by the chromodomain in gene transcription. Biochemistry (2011) 1.10

Structure and chromosomal DNA binding of the SWIRM domain. Nat Struct Mol Biol (2005) 1.06

T cell–derived inducible nitric oxide synthase switches off Th17 cell differentiation. J Exp Med (2013) 1.03

Structural insights into selective histone H3 recognition by the human Polybromo bromodomain 2. Cell Res (2010) 1.02

Tat acetylation: a regulatory switch between early and late phases in HIV transcription elongation. Novartis Found Symp (2004) 1.01

A 14-amino acid sequence with a beta-turn structure is required for apical membrane sorting of the rat ileal bile acid transporter. J Biol Chem (2002) 1.01

Structure of the neural (N-) cadherin prodomain reveals a cadherin extracellular domain-like fold without adhesive characteristics. Structure (2004) 1.01

Grape berry plasma membrane proteome analysis and its differential expression during ripening. J Exp Bot (2008) 0.95

The SUVR4 histone lysine methyltransferase binds ubiquitin and converts H3K9me1 to H3K9me3 on transposon chromatin in Arabidopsis. PLoS Genet (2011) 0.95

Visualization of microvasculature by x-ray in-line phase contrast imaging in rat spinal cord. Phys Med Biol (2012) 0.93

Structure-guided design of potent diazobenzene inhibitors for the BET bromodomains. J Med Chem (2013) 0.93

Biochemical profiling of histone binding selectivity of the yeast bromodomain family. PLoS One (2010) 0.93

Viral-encoded enzymes that target host chromatin functions. Biochim Biophys Acta (2009) 0.93

Computer aided identification of small molecules disrupting uPAR/alpha5beta1--integrin interaction: a new paradigm for metastasis prevention. PLoS One (2009) 0.93

Structure-guided optimization of small molecules inhibiting human immunodeficiency virus 1 Tat association with the human coactivator p300/CREB binding protein-associated factor. J Med Chem (2007) 0.92

Prognostic factors in nasopharyngeal carcinoma with synchronous liver metastasis: a retrospective study for the management of treatment. Radiat Oncol (2013) 0.92

Anti-apoptotic effect of microRNA-21 after contusion spinal cord injury in rats. J Neurotrauma (2013) 0.91

Molecular basis of distinct interactions between Dok1 PTB domain and tyrosine-phosphorylated EGF receptor. J Mol Biol (2004) 0.91

Homology modeling and site-directed mutagenesis to identify selective inhibitors of endothelin-converting enzyme-2. J Med Chem (2008) 0.90

An archaeal SET domain protein exhibits distinct lysine methyltransferase activity towards DNA-associated protein MC1-alpha. FEBS Lett (2005) 0.90

Comparing treatment outcomes of different chemotherapy sequences during intensity modulated radiotherapy for advanced N-stage nasopharyngeal carcinoma patients. Radiat Oncol (2013) 0.90

Solution structure of the Vts1 SAM domain in the presence of RNA. J Mol Biol (2005) 0.90

Dockres: a computer program that analyzes the output of virtual screening of small molecules. Source Code Biol Med (2010) 0.89

Dimerization of a viral SET protein endows its function. Proc Natl Acad Sci U S A (2010) 0.89

Human uroporphyrinogen III synthase: NMR-based mapping of the active site. Proteins (2008) 0.88

Coupling of folding and binding in the PTB domain of the signaling protein Shc. Structure (2003) 0.88

Structural basis for substrate specificity and catalysis of human histone acetyltransferase 1. Proc Natl Acad Sci U S A (2012) 0.88

Rational design of cyclic peptide modulators of the transcriptional coactivator CBP: a new class of p53 inhibitors. J Am Chem Soc (2011) 0.87

Phase II trial of neoadjuvant docetaxel and cisplatin followed by intensity-modulated radiotherapy with concurrent cisplatin in locally advanced nasopharyngeal carcinoma. Cancer Chemother Pharmacol (2013) 0.86

Structure and function of protein modules in chromatin biology. Results Probl Cell Differ (2006) 0.85

βPix plays a dual role in cerebral vascular stability and angiogenesis, and interacts with integrin αvβ8. Dev Biol (2011) 0.85

Structure-guided design of a methyl donor cofactor that controls a viral histone H3 lysine 27 methyltransferase activity. J Med Chem (2011) 0.85

Prevalence of plasmid-mediated quinolone resistance in Escherichia coli isolates in Wenzhou, Southern China, 2002-2008. Jpn J Infect Dis (2011) 0.85

New insights into the catalytic activation of the MAPK phosphatase PAC-1 induced by its substrate MAPK ERK2 binding. J Mol Biol (2005) 0.85

γ-H2AX kinetics as a novel approach to high content screening for small molecule radiosensitizers. PLoS One (2012) 0.83

PTB or not to be: promiscuous, tolerant and Bizarro domains come of age. IUBMB Life (2004) 0.83

Integration of small-molecule discovery in academic biomedical research. Mt Sinai J Med (2010) 0.83

Bromodomain and histone acetyltransferase domain specificities control mixed lineage leukemia phenotype. Cancer Res (2006) 0.82

Modulating molecular functions of p53 with small molecules. Cell Cycle (2006) 0.81

Proposal of a clinical typing system and generation of a prognostic model in patients with nasopharyngeal carcinoma from Southern China. J BUON (2014) 0.81

Structure of the adaptor protein p14 reveals a profilin-like fold with distinct function. J Mol Biol (2005) 0.81

Structural insights into piRNA recognition by the human PIWI-like 1 PAZ domain. Proteins (2011) 0.80

FRS2 PTB domain conformation regulates interactions with divergent neurotrophic receptors. J Biol Chem (2002) 0.80