ArticleNucleic acids research2012
Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 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
116 citing papers in PubMed, 181 citations in OpenAlex.
- Two D-loop resolution systems enable natural genetic transformation in bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Structural and biochemical characterization of a novel DinG containing an endonuclease domain.Cellular and molecular life sciences : CMLS · 2026Article
- CDIN1-Codanin-1 complex defective in congenital dyserythropoietic anaemia type I is an RNA nuclease.Nature communications · 2026Article
- The antiphage mechanism of a widespread trypsin-MBL defense module.Nature chemical biology · 2026Article
- Phage-encoded factor stimulates DNA degradation by the Hna anti-phage defense system.Nature communications · 2026Article
- Structural and mechanistic insights into the dual-nuclease defense protein Upx as an anti-phage system.Nature communications · 2026Article
- Cytosine methylation contributes to the fitness ofiScience · 2026Article
- A phage protein screen identifies triggers of the bacterial innate immune system.Nature microbiology · 2026Article
- The two-component nuclease-active KELShedu system confers broad antiphage activity via abortive infection.Science advances · 2025Article
- The Viral AlphaFold Database of monomers and homodimers reveals conserved protein folds in viruses of bacteria, archaea, and eukaryotes.Science advances · 2025Article
- Article
- YprA family helicases provide the missing link between diverse prokaryotic immune systems.bioRxiv : the preprint server for biology · 2025Article
- West African-South American pandemic Vibrio cholerae encodes multiple distinct phage defence systems.Nature microbiology · 2025Article
- Cyanobacterial Argonautes and Cas4 family nucleases cooperate to interfere with invading DNA.Molecular cell · 2025Article
- Bacterial Hachiman complex executes DNA cleavage for antiphage defense.Nature communications · 2025Article
- Structure, function and evolution of the bacterial DinG-like proteins.Computational and structural biotechnology journal · 2025Review
- Novel Nuclease MbovP701 with a Yqaj Domain Is Interrelated with the Growth ofMicroorganisms · 2024Article
- Gamma-Mobile-Trio systems are mobile elements rich in bacterial defensive and offensive tools.Nature microbiology · 2024Article
- Structural Catalytic Core in Subtilisin-like Proteins and Its Comparison to Trypsin-like Serine Proteases and Alpha/Beta-Hydrolases.International journal of molecular sciences · 2024Review
- Article
56 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Proteins belonging to PD-(D/E)XK phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, DNA repair and tRNA-intron splicing. Their malfunction in humans triggers severe diseases, such as Fanconi anemia and Xeroderma pigmentosum. To date there have been several attempts to identify and classify new PD-(D/E)KK phosphodiesterases using remote homology detection methods. Such efforts are complicated, because the superfamily exhibits extreme sequence and structural divergence. Using advanced homology detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses, we provide a comprehensive reclassification of proteins containing a PD-(D/E)XK domain. The PD-(D/E)XK phosphodiesterases span over 21,900 proteins, which can be classified into 121 groups of various families. Eleven of them, including DUF4420, DUF3883, DUF4263, COG5482, COG1395, Tsp45I, HaeII, Eco47II, ScaI, HpaII and Replic_Relax, are newly assigned to the PD-(D/E)XK superfamily. Some groups of PD-(D/E)XK proteins are present in all domains of life, whereas others occur within small numbers of organisms. We observed multiple horizontal gene transfers even between human pathogenic bacteria or from Prokaryota to Eukaryota. Uncommon domain arrangements greatly elaborate the PD-(D/E)XK world. These include domain architectures suggesting regulatory roles in Eukaryotes, like stress sensing and cell-cycle regulation. Our results may inspire further experimental studies aimed at identification of exact biological functions, specific substrates and molecular mechanisms of reactions performed by these highly diverse 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.