Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-beta effectors.

PubWeight™: 1.06‹?› | Rank: Top 15%

🔗 View Article (PMC 2879523)

Published in Nucleic Acids Res on February 10, 2010

Authors

Nithya BabuRajendran1, Paaventhan Palasingam, Kamesh Narasimhan, Wenjie Sun, Shyam Prabhakar, Ralf Jauch, Prasanna R Kolatkar

Author Affiliations

1: Laboratory of Structural Biochemistry, Genome Institute of Singapore, 60 Biopolis Street, Singapore.

Articles citing this

TGFβ signalling in context. Nat Rev Mol Cell Biol (2012) 8.08

ChIP-seq reveals cell type-specific binding patterns of BMP-specific Smads and a novel binding motif. Nucleic Acids Res (2011) 1.55

Structural determinants of Smad function in TGF-β signaling. Trends Biochem Sci (2015) 1.18

Transforming growth factor β inhibits bone morphogenetic protein-induced transcription through novel phosphorylated Smad1/5-Smad3 complexes. Mol Cell Biol (2012) 1.11

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements. Nucleic Acids Res (2012) 1.11

Genome-wide mechanisms of Smad binding. Oncogene (2012) 1.02

Subtle changes in motif positioning cause tissue-specific effects on robustness of an enhancer's activity. PLoS Genet (2014) 0.92

Zinc depletion causes multiple defects in ovarian function during the periovulatory period in mice. Endocrinology (2011) 0.92

Structural basis for the cooperative DNA recognition by Smad4 MH1 dimers. Nucleic Acids Res (2011) 0.91

A genome-wide screen for genetic variants that modify the recruitment of REST to its target genes. PLoS Genet (2012) 0.86

DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors. Nucleic Acids Res (2015) 0.85

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains. Sci Rep (2015) 0.81

Cooperative assembly of Co-Smad4 MH1 with R-Smad1/3 MH1 on DNA: a molecular dynamics simulation study. PLoS One (2013) 0.80

Structural basis for the Smad5 MH1 domain to recognize different DNA sequences. Nucleic Acids Res (2015) 0.76

Changing POU dimerization preferences converts Oct6 into a pluripotency inducer. EMBO Rep (2016) 0.76

Structural Insights into c-Myc Interacting Zinc Finger Protein-1 (Miz-1) Delineate Domains Required for DNA Scanning and Sequence-specific Binding. J Biol Chem (2016) 0.75

SOXE neofunctionalization and elaboration of the neural crest during chordate evolution. Sci Rep (2016) 0.75

SnoN Stabilizes the SMAD3/SMAD4 Protein Complex. Sci Rep (2017) 0.75

Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq. Nucleic Acids Res (2016) 0.75

Articles cited by this

Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr (2004) 227.01

The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr (1994) 187.88

Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr (1998) 169.28

Phaser crystallographic software. J Appl Crystallogr (2007) 108.34

T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol (2000) 57.88

TGF-beta signal transduction. Annu Rev Biochem (1998) 17.83

Smad transcription factors. Genes Dev (2005) 13.43

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res (2003) 10.63

Direct binding of Smad3 and Smad4 to critical TGF beta-inducible elements in the promoter of human plasminogen activator inhibitor-type 1 gene. EMBO J (1998) 10.01

Diversity and complexity in DNA recognition by transcription factors. Science (2009) 9.07

Transcriptional control by the TGF-beta/Smad signaling system. EMBO J (2000) 8.49

TGFbeta-SMAD signal transduction: molecular specificity and functional flexibility. Nat Rev Mol Cell Biol (2007) 6.34

Recent developments in the PHENIX software for automated crystallographic structure determination. J Synchrotron Radiat (2003) 6.28

Human Smad3 and Smad4 are sequence-specific transcription activators. Mol Cell (1998) 5.88

The TGF-beta superfamily: new members, new receptors, and new genetic tests of function in different organisms. Genes Dev (1994) 5.65

Receptor-associated Mad homologues synergize as effectors of the TGF-beta response. Nature (1996) 5.30

A robust bulk-solvent correction and anisotropic scaling procedure. Acta Crystallogr D Biol Crystallogr (2005) 4.82

Nuclear CDKs drive Smad transcriptional activation and turnover in BMP and TGF-beta pathways. Cell (2009) 4.81

MADR2 is a substrate of the TGFbeta receptor and its phosphorylation is required for nuclear accumulation and signaling. Cell (1996) 4.70

A transcriptional partner for MAD proteins in TGF-beta signalling. Nature (1996) 4.26

MADR1, a MAD-related protein that functions in BMP2 signaling pathways. Cell (1996) 3.87

Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-beta signaling. Cell (1998) 3.86

Drosophila Mad binds to DNA and directly mediates activation of vestigial by Decapentaplegic. Nature (1997) 3.34

Identification and functional characterization of a Smad binding element (SBE) in the JunB promoter that acts as a transforming growth factor-beta, activin, and bone morphogenetic protein-inducible enhancer. J Biol Chem (1998) 3.23

Smads and early developmental signaling by the TGFbeta superfamily. Genes Dev (1998) 3.07

Signaling inputs converge on nuclear effectors in TGF-beta signaling. Trends Biochem Sci (2000) 2.24

Direct binding of Smad1 and Smad4 to two distinct motifs mediates bone morphogenetic protein-specific transcriptional activation of Id1 gene. J Biol Chem (2001) 1.99

Gateway vectors for the production of combinatorially-tagged His6-MBP fusion proteins in the cytoplasm and periplasm of Escherichia coli. Protein Sci (2005) 1.98

Crystal structure of a phosphorylated Smad2. Recognition of phosphoserine by the MH2 domain and insights on Smad function in TGF-beta signaling. Mol Cell (2001) 1.95

A phylogenetically conserved cis-regulatory module in the Msx2 promoter is sufficient for BMP-dependent transcription in murine and Drosophila embryos. Development (2004) 1.94

Regulation of Smad7 promoter by direct association with Smad3 and Smad4. J Biol Chem (1999) 1.88

Smad6 is a Smad1/5-induced smad inhibitor. Characterization of bone morphogenetic protein-responsive element in the mouse Smad6 promoter. J Biol Chem (2000) 1.87

Characterization of a bone morphogenetic protein-responsive Smad-binding element. Mol Biol Cell (2000) 1.66

Structural basis of heteromeric smad protein assembly in TGF-beta signaling. Mol Cell (2004) 1.64

Structure of the forkhead domain of FOXP2 bound to DNA. Structure (2006) 1.61

Transcriptional regulation of BMP4 synexpression in transgenic Xenopus. EMBO J (2004) 1.60

Smad5 and DPC4 are key molecules in mediating BMP-2-induced osteoblastic differentiation of the pluripotent mesenchymal precursor cell line C2C12. J Biol Chem (1998) 1.54

Modeling and analysis of MH1 domain of Smads and their interaction with promoter DNA sequence motif. J Mol Graph Model (2008) 1.50

The solubility and stability of recombinant proteins are increased by their fusion to NusA. Biochem Biophys Res Commun (2004) 1.45

Crystal structure and DNA binding of the homeodomain of the stem cell transcription factor Nanog. J Mol Biol (2007) 1.35

Distinct oligomeric states of SMAD proteins in the transforming growth factor-beta pathway. J Biol Chem (2000) 1.35

Antagonism between Smad1 and Smad2 signaling determines the site of distal visceral endoderm formation in the mouse embryo. J Cell Biol (2009) 1.25

Quantitative analysis of protein-protein interactions. Methods Mol Biol (2004) 1.15

Features of a Smad3 MH1-DNA complex. Roles of water and zinc in DNA binding. J Biol Chem (2003) 1.11

Structural basis of Smad1 activation by receptor kinase phosphorylation. Mol Cell (2001) 1.08

Bone morphogenetic protein-2 (BMP-2) transactivates Dlx3 through Smad1 and Smad4: alternative mode for Dlx3 induction in mouse keratinocytes. Nucleic Acids Res (2002) 1.05

Phylogenetic footprinting and genome scanning identify vertebrate BMP response elements and new target genes. Dev Biol (2005) 0.99

Crystal structures of the Mnk2 kinase domain reveal an inhibitory conformation and a zinc binding site. Structure (2005) 0.99

The structure of Sox17 bound to DNA reveals a conserved bending topology but selective protein interaction platforms. J Mol Biol (2009) 0.96

Smad1 and Smad4 are components of the bone morphogenetic protein-4 (BMP-4)-induced transcription complex of the Xvent-2B promoter. J Biol Chem (2000) 0.94

Characterization of zebrafish smad1, smad2 and smad5: the amino-terminus of smad1 and smad5 is required for specific function in the embryo. Mech Dev (1999) 0.93

Characterization of a Smad motif similar to Drosophila mad in the mouse Msx 1 promoter. Biochem Biophys Res Commun (2002) 0.87

The amino terminus of Smads permits transcriptional specificity. Dev Biol (2001) 0.86

Mouse smad8 phosphorylation downstream of BMP receptors ALK-2, ALK-3, and ALK-6 induces its association with Smad4 and transcriptional activity. Biochem Biophys Res Commun (2000) 0.86

Decapentaplegic-responsive silencers contain overlapping mad-binding sites. J Biol Chem (2006) 0.83

Alpha-helix 2 in the amino-terminal mad homology 1 domain is responsible for specific DNA binding of Smad3. J Biol Chem (2001) 0.81

Crystal optimization and preliminary diffraction data analysis of the Smad1 MH1 domain bound to a palindromic SBE DNA element. Acta Crystallogr Sect F Struct Biol Cryst Commun (2009) 0.80

Flexible interaction of Drosophila Smad complexes with bipartite binding sites. Biochim Biophys Acta (2007) 0.80

Articles by these authors

In vivo enhancer analysis of human conserved non-coding sequences. Nature (2006) 10.60

Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat Genet (2008) 3.55

Integrative model of genomic factors for determining binding site selection by estrogen receptor-α. Mol Syst Biol (2010) 2.04

Assessment of CASP7 structure predictions for template free targets. Proteins (2007) 1.98

Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer. Blood (2007) 1.82

MLL fusion proteins preferentially regulate a subset of wild-type MLL target genes in the leukemic genome. Blood (2011) 1.74

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences. Proc Natl Acad Sci U S A (2005) 1.68

The DNA sequence and comparative analysis of human chromosome 5. Nature (2004) 1.62

Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A. Proc Natl Acad Sci U S A (2005) 1.52

Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny. Hum Mol Genet (2005) 1.49

Improved neovascularization and wound repair by targeting human basic fibroblast growth factor (bFGF) to fibrin. J Mol Med (Berl) (2008) 1.46

In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures. Dev Cell (2013) 1.43

The sequence and analysis of duplication-rich human chromosome 16. Nature (2004) 1.38

Crystal structure and DNA binding of the homeodomain of the stem cell transcription factor Nanog. J Mol Biol (2007) 1.35

Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm. EMBO J (2013) 1.35

Ncoa3 functions as an essential Esrrb coactivator to sustain embryonic stem cell self-renewal and reprogramming. Genes Dev (2012) 1.34

Distinct transcriptional regulatory modules underlie STAT3's cell type-independent and cell type-specific functions. Nucleic Acids Res (2013) 1.21

Mutational dynamics of the SARS coronavirus in cell culture and human populations isolated in 2003. BMC Infect Dis (2004) 1.21

Conversion of Sox17 into a pluripotency reprogramming factor by reengineering its association with Oct4 on DNA. Stem Cells (2011) 1.21

Uniform, optimal signal processing of mapped deep-sequencing data. Nat Biotechnol (2013) 1.17

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements. Nucleic Acids Res (2012) 1.11

Conserved codon composition of ribosomal protein coding genes in Escherichia coli, Mycobacterium tuberculosis and Saccharomyces cerevisiae: lessons from supervised machine learning in functional genomics. Nucleic Acids Res (2002) 1.08

A unique Oct4 interface is crucial for reprogramming to pluripotency. Nat Cell Biol (2013) 1.08

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons. Genome Biol (2007) 1.08

Homogeneous osteogenesis and bone regeneration by demineralized bone matrix loading with collagen-targeting bone morphogenetic protein-2. Biomaterials (2006) 1.07

The effect of crosslinking heparin to demineralized bone matrix on mechanical strength and specific binding to human bone morphogenetic protein-2. Biomaterials (2008) 1.04

Evolution of the vertebrate gene regulatory network controlled by the transcriptional repressor REST. Mol Biol Evol (2009) 1.02

Collagen-targeting vascular endothelial growth factor improves cardiac performance after myocardial infarction. Circulation (2009) 1.02

Lack of Cul4b, an E3 ubiquitin ligase component, leads to embryonic lethality and abnormal placental development. PLoS One (2012) 1.00

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers. Genome Res (2013) 0.97

The crystal structure of the Sox4 HMG domain-DNA complex suggests a mechanism for positional interdependence in DNA recognition. Biochem J (2012) 0.96

The structure of Sox17 bound to DNA reveals a conserved bending topology but selective protein interaction platforms. J Mol Biol (2009) 0.96

Linear ordered collagen scaffolds loaded with collagen-binding brain-derived neurotrophic factor improve the recovery of spinal cord injury in rats. Tissue Eng Part A (2009) 0.94

Primate-specific evolution of an LDLR enhancer. Genome Biol (2006) 0.94

Identification and characterization of a novel mutation in the carbonic anhydrase IV gene that causes retinitis pigmentosa. Invest Ophthalmol Vis Sci (2007) 0.92

Human accelerated region 1 noncoding RNA is repressed by REST in Huntington's disease. Physiol Genomics (2010) 0.92

Gene therapy with tumor-specific promoter mediated suicide gene plus IL-12 gene enhanced tumor inhibition and prolonged host survival in a murine model of Lewis lung carcinoma. J Transl Med (2011) 0.91

Purification, crystallization and preliminary X-ray diffraction analysis of the HMG domain of Sox17 in complex with DNA. Acta Crystallogr Sect F Struct Biol Cryst Commun (2008) 0.91

The effect of collagen-targeting platelet-derived growth factor on cellularization and vascularization of collagen scaffolds. Biomaterials (2006) 0.91

Polyethyleneimine-mediated synthesis of folic acid-targeted iron oxide nanoparticles for in vivo tumor MR imaging. Biomaterials (2013) 0.91

Structural basis for the cooperative DNA recognition by Smad4 MH1 dimers. Nucleic Acids Res (2011) 0.91

TherMos: Estimating protein-DNA binding energies from in vivo binding profiles. Nucleic Acids Res (2013) 0.90

A 1.7A structure of Fve, a member of the new fungal immunomodulatory protein family. J Mol Biol (2003) 0.90

Crosslinked three-dimensional demineralized bone matrix for the adipose-derived stromal cell proliferation and differentiation. Tissue Eng Part A (2009) 0.89

Crystal structure of the dimeric Oct6 (POU3f1) POU domain bound to palindromic MORE DNA. Proteins (2011) 0.88

Co-motif discovery identifies an Esrrb-Sox2-DNA ternary complex as a mediator of transcriptional differences between mouse embryonic and epiblast stem cells. Stem Cells (2013) 0.88

In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column. BMC Genomics (2014) 0.87

Moderate alcohol use and mortality from ischaemic heart disease: a prospective study in older Chinese people. PLoS One (2008) 0.86

Association of mitochondrial DNA copy number in peripheral blood leukocytes with risk of esophageal adenocarcinoma. Carcinogenesis (2013) 0.86

A genome-wide screen for genetic variants that modify the recruitment of REST to its target genes. PLoS Genet (2012) 0.86

Sox transcription factors require selective interactions with Oct4 and specific transactivation functions to mediate reprogramming. Stem Cells (2013) 0.85

Purification and characterization of phenoloxidase from crab Charybdis japonica. Fish Shellfish Immunol (2006) 0.85

Structural analysis and dimerization profile of the SCAN domain of the pluripotency factor Zfp206. Nucleic Acids Res (2012) 0.84

Crosslinking heparin to collagen scaffolds for the delivery of human platelet-derived growth factor. J Biomed Mater Res B Appl Biomater (2009) 0.84

Identification of a polyoxometalate inhibitor of the DNA binding activity of Sox2. ACS Chem Biol (2011) 0.84

Novel nerve guidance material prepared from bovine aponeurosis. J Biomed Mater Res A (2006) 0.84

Loading of VEGF to the heparin cross-linked demineralized bone matrix improves vascularization of the scaffold. J Mater Sci Mater Med (2009) 0.82

Adjuvant therapy for T3N0 rectal cancer in the total mesorectal excision era- identification of the high risk patients. Radiat Oncol (2010) 0.82

Implications for domain fusion protein-protein interactions based on structural information. BMC Bioinformatics (2004) 0.82

Compression of functional space in HLA-A sequence diversity. Hum Immunol (2003) 0.82

Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish. PLoS Genet (2013) 0.81

Vascularization and cellularization of collagen scaffolds incorporated with two different collagen-targeting human basic fibroblast growth factors. J Biomed Mater Res A (2007) 0.81

Direct chemical cross-linking of platelet-derived growth factor-BB to the demineralized bone matrix improves cellularization and vascularization. Biomacromolecules (2009) 0.81

Crystal optimization and preliminary diffraction data analysis of the Smad1 MH1 domain bound to a palindromic SBE DNA element. Acta Crystallogr Sect F Struct Biol Cryst Commun (2009) 0.80

Ambient air pollution and depressive symptoms in older adults. Environ Health Perspect (2015) 0.80

Crystallization and preliminary X-ray analysis of candoxin, a novel reversible neurotoxin from the Malayan krait Bungarus candidus. Acta Crystallogr D Biol Crystallogr (2003) 0.80

The bone-derived collagen containing mineralized matrix for the loading of collagen-binding bone morphogenetic protein-2. J Biomed Mater Res A (2009) 0.80

Radiation enhances suicide gene therapy in radioresistant laryngeal squamous cell carcinoma via activation of a tumor-specific promoter. Cancer Lett (2009) 0.79

The SOX transcription factors as key players in pluripotent stem cells. Stem Cells Dev (2014) 0.79

Collagen-binding human epidermal growth factor promotes cellularization of collagen scaffolds. Tissue Eng Part A (2009) 0.79

Cloning, purification and preliminary X-ray data analysis of the human ID2 homodimer. Acta Crystallogr Sect F Struct Biol Cryst Commun (2012) 0.79

Inhibition of anaerobic ammonium oxidizing (anammox) enrichment cultures by substrates, metabolites and common wastewater constituents. Chemosphere (2012) 0.79

Facile one-pot synthesis of Fe3O4@Au composite nanoparticles for dual-mode MR/CT imaging applications. ACS Appl Mater Interfaces (2013) 0.79

Factors associated with household transmission of pandemic (H1N1) 2009 among self-quarantined patients in Beijing, China. PLoS One (2013) 0.79

Identification and functional analysis of a SLC33A1: c.339T>G (p.Ser113Arg) variant in the original SPG42 family. Hum Mutat (2015) 0.78

Facile synthesis of RGD peptide-modified iron oxide nanoparticles with ultrahigh relaxivity for targeted MR imaging of tumors. Biomater Sci (2015) 0.77

Crystallization and preliminary X-ray crystallographic studies on the fungal immunomodulatory protein Fve from the golden needle mushroom (Flammulina velutipes). Acta Crystallogr D Biol Crystallogr (2003) 0.77

Purification and characterization of phenoloxidase from clam Ruditapes philippinarum. Fish Shellfish Immunol (2005) 0.77

Human basic fibroblast growth factor fused with Kringle4 peptide binds to a fibrin scaffold and enhances angiogenesis. Tissue Eng Part A (2009) 0.77

Putative role of Tat-Env interaction in HIV infection. AIDS (2013) 0.76