ArticleScientific reports2015
In silico identification of AMPylating enzymes and study of their divergent evolution.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed.
- The rise of AMPylation: from bacterial beginnings to modern implications in health and disease.Biochemical Society transactions · 2025Review
- The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3.Communications biology · 2023Article
- Infancy-onset diabetes caused by de-regulated AMPylation of the human endoplasmic reticulum chaperone BiP.EMBO molecular medicine · 2023Article
- AMPylation and Endoplasmic Reticulum Protein Folding Homeostasis.Cold Spring Harbor perspectives in biology · 2023Review
- A convolutional neural network based tool for predicting protein AMPylation sites from binary profile representation.Scientific reports · 2022Article
- Production of an Active, Human Membrane Protein inInternational journal of molecular sciences · 2022Article
- Structures of a deAMPylation complex rationalise the switch between antagonistic catalytic activities of FICD.Nature communications · 2021Article
- Investigation of the Detailed AMPylated Reaction Mechanism for the Huntingtin Yeast-Interacting Protein E Enzyme HYPE.International journal of molecular sciences · 2021Article
- Fic and non-Fic AMPylases: protein AMPylation in metazoans.Open biology · 2021Article
- Fe(2)OG: an integrated HMM profile-based web server to predict and analyze putative non-haem iron(II)- and 2-oxoglutarate-dependent dioxygenase function in protein sequences.BMC research notes · 2021Article
- Monoclonal Anti-AMP Antibodies Are Sensitive and Valuable Tools for Detecting Patterns of AMPylation.iScience · 2020Article
- Post-translational modifications of Hsp70 family proteins: Expanding the chaperone code.The Journal of biological chemistry · 2020Review
- An oligomeric state-dependent switch in the ER enzyme FICD regulates AMPylation and deAMPylation of BiP.The EMBO journal · 2019Article
- rAMPing Up Stress Signaling: Protein AMPylation in Metazoans.Trends in cell biology · 2017Review
- FICD acts bifunctionally to AMPylate and de-AMPylate the endoplasmic reticulum chaperone BiP.Nature structural & molecular biology · 2017Article
- Oyster RNA-seq Data Support the Development ofFrontiers in microbiology · 2017Article
- Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- In silico Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases.Frontiers in plant science · 2016Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
AMPylation is a novel post-translational modification (PTM) involving covalent attachment of an AMP moiety to threonine/tyrosine side chains of a protein. AMPylating enzymes belonging to three different families, namely Fic/Doc, GS-ATase and DrrA have been experimentally characterized. Involvement of these novel enzymes in a myriad of biological processes makes them interesting candidates for genome-wide search. We have used SVM and HMM to develop a computational protocol for identification of AMPylation domains and their classification into various functional subfamilies catalyzing AMPylation, deAMPylation, phosphorylation and phosphocholine transfer. Our analysis has not only identified novel PTM catalyzing enzymes among unannotated proteins, but has also revealed how this novel enzyme family has evolved to generate functional diversity by subtle changes in sequence/structures of the proteins. Phylogenetic analysis of Fic/Doc has revealed three new isofunctional subfamilies, thus adding to their functional divergence. Also, frequent occurrence of Fic/Doc proteins on highly mobile and unstable genomic islands indicated their evolution via extensive horizontal gene transfers. On the other hand phylogenetic analyses indicate lateral evolution of GS-ATase family and an early duplication event responsible for AMPylation and deAMPylation activity of GS-ATase. Our analysis also reveals molecular basis of substrate specificity of DrrA proteins.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.