Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family.

PubWeight™: 1.29‹?› | Rank: Top 10%

🔗 View Article (PMC 549199)

Published in BMC Bioinformatics on February 07, 2005

Authors

Maria Novatchkova1, Andreas Bachmair, Birgit Eisenhaber, Frank Eisenhaber

Author Affiliations

1: Gregor Mendel-Institut GMI, Austrian Academy of Sciences, Vienna Biocenter, A-1030 Vienna, Austria. maria.novatchkova@gmi.oeaw.ac.at

Articles citing this

The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition. Nat Rev Mol Cell Biol (2010) 4.72

Regulation of DNA cross-link repair by the Fanconi anemia/BRCA pathway. Genes Dev (2012) 3.42

Discovery, in vivo activity, and mechanism of action of a small-molecule p53 activator. Cancer Cell (2008) 3.38

SUMO-targeted ubiquitin ligases in genome stability. EMBO J (2007) 2.77

Conserved function of RNF4 family proteins in eukaryotes: targeting a ubiquitin ligase to SUMOylated proteins. EMBO J (2007) 2.59

SUMO junction-what's your function? New insights through SUMO-interacting motifs. EMBO Rep (2007) 2.58

Distinct SUMO ligases cooperate with Esc2 and Slx5 to suppress duplication-mediated genome rearrangements. PLoS Genet (2013) 1.67

The Saccharomyces cerevisiae Esc2 and Smc5-6 proteins promote sister chromatid junction-mediated intra-S repair. Mol Biol Cell (2009) 1.44

Regulation of the Fanconi anemia pathway by a SUMO-like delivery network. Genes Dev (2011) 1.28

The Smc5/6 complex and Esc2 influence multiple replication-associated recombination processes in Saccharomyces cerevisiae. Mol Biol Cell (2010) 1.22

Esc2 and Sgs1 act in functionally distinct branches of the homologous recombination repair pathway in Saccharomyces cerevisiae. Mol Biol Cell (2009) 1.22

Heterochromatic breaks move to the nuclear periphery to continue recombinational repair. Nat Cell Biol (2015) 1.15

Molecular mimicry of SUMO promotes DNA repair. Nat Struct Mol Biol (2009) 1.14

SUMO-targeted ubiquitin ligase, Rad60, and Nse2 SUMO ligase suppress spontaneous Top1-mediated DNA damage and genome instability. PLoS Genet (2011) 1.02

Genome stability roles of SUMO-targeted ubiquitin ligases. DNA Repair (Amst) (2009) 1.00

Cul8/Rtt101 forms a variety of protein complexes that regulate DNA damage response and transcriptional silencing. J Biol Chem (2010) 0.99

Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison. New Phytol (2012) 0.88

A SUMO-like domain protein, Esc2, is required for genome integrity and sister chromatid cohesion in Saccharomyces cerevisiae. Genetics (2008) 0.88

Schizosaccharomyces pombe Cds1Chk2 regulates homologous recombination at stalled replication forks through the phosphorylation of recombination protein Rad60. J Cell Sci (2009) 0.82

Shared and unique properties of ubiquitin and SUMO interaction networks in DNA repair. Genes Dev (2011) 0.80

Saccharomyces cerevisiae Esc2p interacts with Sir2p through a small ubiquitin-like modifier (SUMO)-binding motif and regulates transcriptionally silent chromatin in a locus-dependent manner. J Biol Chem (2010) 0.79

Defining the SUMO System in Maize: SUMOylation Is Up-Regulated during Endosperm Development and Rapidly Induced by Stress. Plant Physiol (2016) 0.77

Nup358 binds to AGO proteins through its SUMO-interacting motifs and promotes the association of target mRNA with miRISC. EMBO Rep (2016) 0.75

Esc2 promotes Mus81 complex-activity via its SUMO-like and DNA binding domains. Nucleic Acids Res (2016) 0.75

Characterisation of the SUMO-like domains of Schizosaccharomyces pombe Rad60. PLoS One (2010) 0.75

Pathways and Mechanisms that Prevent Genome Instability in Saccharomyces cerevisiae. Genetics (2017) 0.75

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47

VMD: visual molecular dynamics. J Mol Graph (1996) 117.02

SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol (1995) 74.88

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

Profile hidden Markov models. Bioinformatics (1998) 56.04

The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res (2000) 49.22

Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature (2000) 20.54

SMART 4.0: towards genomic data integration. Nucleic Acids Res (2004) 19.37

CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res (2002) 18.54

Analysis of compositionally biased regions in sequence databases. Methods Enzymol (1996) 17.11

hSIR2(SIRT1) functions as an NAD-dependent p53 deacetylase. Cell (2001) 15.97

Protein modification by SUMO. Annu Rev Biochem (2004) 10.59

Genome evolution in yeasts. Nature (2004) 10.50

NPS@: network protein sequence analysis. Trends Biochem Sci (2000) 9.68

Mammalian SIRT1 represses forkhead transcription factors. Cell (2004) 8.89

Coiled coils: new structures and new functions. Trends Biochem Sci (1996) 8.63

The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res (2000) 6.89

Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci (2000) 6.23

Silencing factors participate in DNA repair and recombination in Saccharomyces cerevisiae. Nature (1997) 4.57

CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics (2004) 4.14

Ubiquitin and its kin: how close are the family ties? Trends Cell Biol (2000) 2.81

SUMO: a regulator of gene expression and genome integrity. Oncogene (2004) 2.68

Structure determination of the small ubiquitin-related modifier SUMO-1. J Mol Biol (1998) 2.66

CAST: an iterative algorithm for the complexity analysis of sequence tracts. Complexity analysis of sequence tracts. Bioinformatics (2000) 2.50

Rapid automatic detection and alignment of repeats in protein sequences. Proteins (2000) 2.35

Hybrid fold recognition: combining sequence derived properties with evolutionary information. Pac Symp Biocomput (2000) 2.28

A histone variant, Htz1p, and a Sir1p-like protein, Esc2p, mediate silencing at HMR. Mol Cell (2000) 2.18

Loopy proteins appear conserved in evolution. J Mol Biol (2002) 1.96

Drosophila Sir2 is required for heterochromatic silencing and by euchromatic Hairy/E(Spl) bHLH repressors in segmentation and sex determination. Cell (2002) 1.81

Novel essential DNA repair proteins Nse1 and Nse2 are subunits of the fission yeast Smc5-Smc6 complex. J Biol Chem (2003) 1.65

From UBA to UBX: new words in the ubiquitin vocabulary. Trends Cell Biol (2002) 1.61

SUMO: of branched proteins and nuclear bodies. Oncogene (2001) 1.52

Replication checkpoint kinase Cds1 regulates recombinational repair protein Rad60. Mol Cell Biol (2003) 1.50

The Schizosaccharomyces pombe rad60 gene is essential for repairing double-strand DNA breaks spontaneously occurring during replication and induced by DNA-damaging agents. Mol Cell Biol (2002) 1.46

Structure of the ubiquitin-interacting motif of S5a bound to the ubiquitin-like domain of HR23B. J Biol Chem (2003) 1.40

Dual role of sumoylation in the nuclear localization and transcriptional activation of NFAT1. J Biol Chem (2004) 1.31

Restoration of silencing in Saccharomyces cerevisiae by tethering of a novel Sir2-interacting protein, Esc8. Genetics (2002) 1.27

NF-AT-Driven interleukin-4 transcription potentiated by NIP45. Science (1996) 1.21

An artificial intelligence approach to motif discovery in protein sequences: application to steriod dehydrogenases. J Steroid Biochem Mol Biol (1997) 1.16

Reconstitution of T cell-specific transcription directed by composite NFAT/Oct elements. J Immunol (2000) 1.11

One-hybrid screens at the Saccharomyces cerevisiae HMR locus identify novel transcriptional silencing factors. Genetics (2004) 0.96

On the properties and sequence context of structurally ambivalent fragments in proteins. Protein Sci (2003) 0.94

The ubiquitin superfamily: members, features, and phylogenies. J Proteome Res (2003) 0.82

Articles by these authors

Fat mobilization in adipose tissue is promoted by adipose triglyceride lipase. Science (2004) 8.58

The Tudor domain 'Royal Family': Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem Sci (2003) 5.19

The WD40 propeller domain of Cdh1 functions as a destruction box receptor for APC/C substrates. Mol Cell (2005) 2.77

TPR subunits of the anaphase-promoting complex mediate binding to the activator protein CDH1. Curr Biol (2003) 2.71

Human Rif1, ortholog of a yeast telomeric protein, is regulated by ATM and 53BP1 and functions in the S-phase checkpoint. Genes Dev (2004) 2.33

Two fission yeast homologs of Drosophila Mei-S332 are required for chromosome segregation during meiosis I and II. Curr Biol (2004) 2.28

The STIR-domain superfamily in signal transduction, development and immunity. Trends Biochem Sci (2003) 2.24

N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. J Mol Biol (2002) 2.18

A sensitive predictor for potential GPI lipid modification sites in fungal protein sequences and its application to genome-wide studies for Aspergillus nidulans, Candida albicans, Neurospora crassa, Saccharomyces cerevisiae and Schizosaccharomyces pombe. J Mol Biol (2004) 2.09

Human Scc4 is required for cohesin binding to chromatin, sister-chromatid cohesion, and mitotic progression. Curr Biol (2006) 2.04

Eco1 is a novel acetyltransferase that can acetylate proteins involved in cohesion. Curr Biol (2002) 2.04

Kleisins: a superfamily of bacterial and eukaryotic SMC protein partners. Mol Cell (2003) 1.85

Refinement and prediction of protein prenylation motifs. Genome Biol (2005) 1.84

Prediction of peroxisomal targeting signal 1 containing proteins from amino acid sequence. J Mol Biol (2003) 1.83

Glycosylphosphatidylinositol lipid anchoring of plant proteins. Sensitive prediction from sequence- and genome-wide studies for Arabidopsis and rice. Plant Physiol (2003) 1.72

N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. J Mol Biol (2002) 1.72

Mapping the sequence mutations of the 2009 H1N1 influenza A virus neuraminidase relative to drug and antibody binding sites. Biol Direct (2009) 1.70

Phosphorylation-induced autoinhibition regulates the cytoskeletal protein Lethal (2) giant larvae. Curr Biol (2005) 1.65

Chromosomal map of the model legume Lotus japonicus. Genetics (2002) 1.60

The ring between ring fingers (RBR) protein family. Genome Biol (2007) 1.59

Towards complete sets of farnesylated and geranylgeranylated proteins. PLoS Comput Biol (2007) 1.57

Motif refinement of the peroxisomal targeting signal 1 and evaluation of taxon-specific differences. J Mol Biol (2003) 1.51

Myristoylation of viral and bacterial proteins. Trends Microbiol (2004) 1.49

pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model. Biol Direct (2007) 1.46

Enzymes and auxiliary factors for GPI lipid anchor biosynthesis and post-translational transfer to proteins. Bioessays (2003) 1.45

The N-end rule pathway promotes seed germination and establishment through removal of ABA sensitivity in Arabidopsis. Proc Natl Acad Sci U S A (2009) 1.44

Crystal structure of the p14/MP1 scaffolding complex: how a twin couple attaches mitogen-activated protein kinase signaling to late endosomes. Proc Natl Acad Sci U S A (2004) 1.43

MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins. Genome Biol (2004) 1.42

TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. Bioinformatics (2004) 1.37

A new common mutation in the hemagglutinin of the 2009 (H1N1) influenza A virus. PLoS Curr (2010) 1.37

On filtering false positive transmembrane protein predictions. Protein Eng (2002) 1.35

RNAase-III enzyme Dicer maintains signaling pathways for differentiation and survival in mouse cortical neural stem cells. J Cell Sci (2010) 1.33

The highly pathogenic H7N3 avian influenza strain from July 2012 in Mexico acquired an extended cleavage site through recombination with host 28S rRNA. Virol J (2013) 1.33

S. pombe meiotic linear elements contain proteins related to synaptonemal complex components. J Cell Sci (2004) 1.31

Ubiquitin lysine 63 chain forming ligases regulate apical dominance in Arabidopsis. Plant Cell (2007) 1.30

More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology. PLoS Comput Biol (2010) 1.26

Lysine63-linked ubiquitylation of PIN2 auxin carrier protein governs hormonally controlled adaptation of Arabidopsis root growth. Proc Natl Acad Sci U S A (2012) 1.19

ANNIE: integrated de novo protein sequence annotation. Nucleic Acids Res (2009) 1.19

Molecular processes during fat cell development revealed by gene expression profiling and functional annotation. Genome Biol (2005) 1.16

Beware of moving targets: reference proteome content fluctuates substantially over the years. J Bioinform Comput Biol (2012) 1.16

Repression of the floral transition via histone H2B monoubiquitination. Plant J (2008) 1.15

Extending Asia Pacific bioinformatics into new realms in the "-omics" era. BMC Genomics (2009) 1.15

Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1. Nucleic Acids Res (2003) 1.14

A genetic linkage map of the model legume Lotus japonicus and strategies for fast mapping of new loci. Genetics (2002) 1.12

Protein prenyltransferases. Genome Biol (2003) 1.11

Substrates related to chromatin and to RNA-dependent processes are modified by Arabidopsis SUMO isoforms that differ in a conserved residue with influence on desumoylation. Plant Physiol (2009) 1.10

PRT6/At5g02310 encodes an Arabidopsis ubiquitin ligase of the N-end rule pathway with arginine specificity and is not the CER3 locus. FEBS Lett (2007) 1.09

SNEV is an evolutionarily conserved splicing factor whose oligomerization is necessary for spliceosome assembly. Nucleic Acids Res (2005) 1.08

Posttranslational modifications and subcellular localization signals: indicators of sequence regions without inherent 3D structure? Curr Protein Pept Sci (2007) 1.08

SUMO conjugation in plants. Planta (2004) 1.07

Experimental testing of predicted myristoylation targets involved in asymmetric cell division and calcium-dependent signalling. Cell Cycle (2008) 1.06

PRT1 of Arabidopsis is a ubiquitin protein ligase of the plant N-end rule pathway with specificity for aromatic amino-terminal residues. Plant Physiol (2003) 1.05

Linking transcriptional mediators via the GACKIX domain super family. Curr Biol (2004) 1.02

Species specific membrane anchoring of nyctalopin, a small leucine-rich repeat protein. Hum Mol Genet (2005) 1.00

The substrate specificity profile of human granzyme A. Biol Chem (2010) 0.98

Genome-wide loss-of-function analysis of deubiquitylating enzymes for zebrafish development. BMC Genomics (2009) 0.97

Synthesizing non-natural parts from natural genomic template. J Biol Eng (2009) 0.95

Prediction of posttranslational modification of proteins from their amino acid sequence. Methods Mol Biol (2010) 0.94

All that glitters is not gold--founder effects complicate associations of flu mutations to disease severity. Virol J (2010) 0.93

Powerful sequence similarity search methods and in-depth manual analyses can identify remote homologs in many apparently "orphan" viral proteins. J Virol (2013) 0.93

Structural requirements for interaction of peroxisomal targeting signal 2 and its receptor PEX7. J Biol Chem (2011) 0.93

Prediction of sequence signals for lipid post-translational modifications: insights from case studies. Proteomics (2004) 0.93

Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins. Biol Direct (2011) 0.92

Hidden localization motifs: naturally occurring peroxisomal targeting signals in non-peroxisomal proteins. Genome Biol (2004) 0.92

Protein prenyltransferases: anchor size, pseudogenes and parasites. Biol Chem (2003) 0.92

Farnesylation or geranylgeranylation? Efficient assays for testing protein prenylation in vitro and in vivo. BMC Biochem (2006) 0.91

Gitelman syndrome. Hypertension (2009) 0.90

Update on sumoylation: defining core components of the plant SUMO conjugation system by phylogenetic comparison. New Phytol (2012) 0.88

Lotus burttii takes a position of the third corner in the lotus molecular genetics triangle. DNA Res (2005) 0.88

Cleaning of raw peptide MS/MS spectra: improved protein identification following deconvolution of multiply charged peaks, isotope clusters, and removal of background noise. Proteomics (2006) 0.88

Parameterization of disorder predictors for large-scale applications requiring high specificity by using an extended benchmark dataset. BMC Genomics (2010) 0.88

On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation. Biol Direct (2008) 0.87

Application of a sensitive collection heuristic for very large protein families: evolutionary relationship between adipose triglyceride lipase (ATGL) and classic mammalian lipases. BMC Bioinformatics (2006) 0.87

Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPARγ. Cell Mol Life Sci (2010) 0.87

A new piece in the puzzle of the novel avian-origin influenza A (H7N9) virus. Biol Direct (2013) 0.87

Nuclear import of a lipid-modified transcription factor: mobilization of NFAT5 isoform a by osmotic stress. Cell Cycle (2011) 0.86

SPACER: Server for predicting allosteric communication and effects of regulation. Nucleic Acids Res (2013) 0.86

A CH domain-containing N terminus in NuMA? Protein Sci (2002) 0.85

Key roles of the Escherichia coli AhpC C-terminus in assembly and catalysis of alkylhydroperoxide reductase, an enzyme essential for the alleviation of oxidative stress. Biochim Biophys Acta (2014) 0.84

Biomolecular pathway databases. Methods Mol Biol (2010) 0.84

Structural insight into the glycosylphosphatidylinositol transamidase subunits PIG-K and PIG-S from yeast. J Struct Biol (2010) 0.83

Elevated salicylic acid levels conferred by increased expression of ISOCHORISMATE SYNTHASE 1 contribute to hyperaccumulation of SUMO1 conjugates in the Arabidopsis mutant early in short days 4. Plant J (2014) 0.83

Distinct roles for Arabidopsis SUMO protease ESD4 and its closest homolog ELS1. Planta (2010) 0.83

Databases of protein-protein interactions and complexes. Methods Mol Biol (2010) 0.83

Transcriptional regulation of nitrate assimilation in Pseudomonas aeruginosa occurs via transcriptional antitermination within the nirBD-PA1779-cobA operon. Microbiology (2012) 0.82