Phospho.ELM: a database of phosphorylation sites--update 2011

Dinkel, Holger; Chica, Claudia; Via, Allegra; Gould, Cathryn M.; Jensen, Lars Juhl; Gibson, Toby J.; Diella, Francesca

doi:10.1093/nar/gkq1104

Cited by 596 publications

(497 citation statements)

References 53 publications

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“…Therefore, we initially applied the same minimal network extraction technique used in yeast to a high quality human interactome on the basis of known human kinase substrates (seed nodes) (Figure 4c). We used a global binary human protein interaction network (9,412 proteins, 33,646 PPIs, Data S2 (Woodsmith and Stelzl, 2014)), and collected known kinase-substrate relationships from literature databases (Dinkel et al, 2011;Hornbeck et al, 2012). The number of known kinase-substrate pairs varied from 0 (TNK1) to about 200 substrates reported for Src kinase in the databases.…”

Section: Network Inference To Identify Putative Human Py Kinase Substmentioning

confidence: 99%

Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate

et al. 2017

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Systematic assessment of tyrosine kinase-substrate relationships is fundamental to a better understanding of cellular signaling and its profound alterations in human diseases such as cancer. In human cells, complex signaling networks, feedback loops, conditional activity and intra-kinase redundancy combine to confound systematic attempts to address this topic. We leveraged the model organism S. cerevisiae to individually express human non-receptor tyrosine kinases (NRTKs) and exploited the full yeast proteome as an in vivo model substrate. For 16 NRTKs, we recorded 3,279 kinase-substrate relationships involving 1,351 yeast pY-sites. From this data we generated a set of new linear kinase motifs and assigned ~1,300 known human pY-sites to specific NRTKs. Furthermore, experimentally defined pY-sites for each individual kinase were shown to cluster within the yeast interactome network irrespective of linear motif information. We therefore applied a network inference approach to predict kinase-substrate relationships for more than 3,500 human proteins, marking a substantial step forward in our understanding of kinase biology.. Corwin et al., revised3 7/25/2017 3

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Section: Network Inference To Identify Putative Human Py Kinase Substmentioning

confidence: 99%

Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate

et al. 2017

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“…Numerous ULM-associated phosphorylation sites remain to be investigated. In a striking example, abundant phosphorylated threonine-proline (TP) motifs riddle the N-terminal IDR of SF3b155, including 29 TP sequences of which 18 are experimentally verified, phosphorylation sites in the Phospho.ELM database (Dinkel et al 2011). The U2AF 65 and MAN1 ULMs also contain single TP motifs, whereas the SF1 and ATX1 ULMs have none.…”

Section: Ulm Phosphorylation Regulates Partnerships With Uhmsmentioning

confidence: 99%

Unmasking the U2AF homology motif family: a bona fide protein–protein interaction motif in disguise

Loerch

Kielkopf

2016

RNA

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U2AF homology motifs (UHM) that recognize U2AF ligand motifs (ULM) are an emerging family of protein-protein interaction modules. UHM-ULM interactions recur in pre-mRNA splicing factors including U2AF1 and SF3b1, which are frequently mutated in myelodysplastic syndromes. The core topology of the UHM resembles an RNA recognition motif and is often mistakenly classified within this large family. Here, we unmask the charade and review recent discoveries of UHM-ULM modules for protein-protein interactions. Diverse polypeptide extensions and selective phosphorylation of UHM and ULM family members offer new molecular mechanisms for the assembly of specific partners in the early-stage spliceosome.

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“…As input data for the predictions, we used an in-house curated database (KinomeXplorer-DB), which collects known phosphorylation sites from public resources such as Phospho.ELM (18), PhosphoSitePlus (19), and PhosphoGRID (http://www.phosphogrid.org/). In the current version, there are 64,232 phosphorylation sites available, for each of which we predicted the most likely phosphorylating kinases.…”

Section: Haspin and Cenp-t Proteins Production And Purificationhaspinmentioning

confidence: 99%

Modulation of the Chromatin Phosphoproteome by the Haspin Protein Kinase

Maiolica

Medina-Redondo

Schoof

et al. 2014

Molecular & Cellular Proteomics

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Recent discoveries have highlighted the importance of Haspin kinase activity for the correct positioning of the kinase Aurora B at the centromere. Haspin phosphorylates Thr 3 of the histone H3 (H3), which provides a signal for Aurora B to localize to the centromere of mitotic chromosomes. To date, histone H3 is the only confirmed Haspin substrate. We used a combination of biochemical, pharmacological, and mass spectrometric approaches to study the consequences of Haspin inhibition in mitotic cells. We quantified 3964 phosphorylation sites on chromatin-associated proteins and identified a Haspin protein-protein interaction network. We determined the Haspin consensus motif and the co-crystal structure of the kinase with the histone H3 tail.

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Phospho.ELM: a database of phosphorylation sites--update 2011

Cited by 596 publications

References 53 publications

Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate

Defining Human Tyrosine Kinase Phosphorylation Networks Using Yeast as an In Vivo Model Substrate

Unmasking the U2AF homology motif family: a bona fide protein–protein interaction motif in disguise

Modulation of the Chromatin Phosphoproteome by the Haspin Protein Kinase

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