ReviewJournal of bacteriology2022
Sequence Conservation, Domain Architectures, and Phylogenetic Distribution of the HD-GYP Type c-di-GMP Phosphodiesterases.
Review in Journal of bacteriology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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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.
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Who cites it
23 citing papers in PubMed, 22 citations in OpenAlex.
- Research on the Potential Mechanism of Guanine Nucleotides Enhancing the Tolerance ofFoods (Basel, Switzerland) · 2026Article
- Dual-function enzyme acts as a global c-di-GMP sink and local anti sigma factor antagonist to drive cellular differentiation.PLoS genetics · 2026Article
- Structural analyses uncover protease-adhesin interactions and c-di-GMP receptor regulation in sulfate-reducing bacteria.Nature communications · 2026Article
- Genomic and physiological characterization of Aliivibrio sp. REG001485: A specialized functional ecotype for long-term bioluminescent signaling.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2026Article
- Discovery of Novel c-di-GMP-Related Genes inPathogens (Basel, Switzerland) · 2026Article
- Complete degradation of polycyclic antibiotic methacycline by a micro/nanostructured biogenic Mn oxide composite from engineered Mn(II)-oxidizingMicrobiology spectrum · 2025Article
- Structural and functional diversity of sensor domains in bacterial transmembrane receptors.Trends in microbiology · 2025Review
- Genetic Dissection of Cyclic di-GMP Signalling in Pseudomonas aeruginosa via Systematic Diguanylate Cyclase Disruption.Microbial biotechnology · 2025Article
- Cyclic Diguanylate in the Wild: Roles During Plant and Animal Colonization.Annual review of microbiology · 2024Review
- Reconstitution of a biofilm adhesin system from a sulfate-reducing bacterium inProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Roles and Regulation of Quorum Sensing of Acidophiles in Bioleaching: A Review.Microorganisms · 2024Review
- pGpG-signaling regulates virulence and global transcriptomic targets inbioRxiv : the preprint server for biology · 2024Article
- The small protein MntS evolved from a signal peptide and acquired a novel function regulating manganese homeostasis in Escherichia coli.Molecular microbiology · 2024Article
- Reconstitution of a Biofilm Adhesin System from a Sulfate-Reducing Bacterium inbioRxiv : the preprint server for biology · 2023Article
- Gas and light: triggers of c-di-GMP-mediated regulation.FEMS microbiology reviews · 2023Review
- All DACs in a Row: Domain Architectures of Bacterial and Archaeal Diadenylate Cyclases.Journal of bacteriology · 2023Review
- Recent advances and perspectives in nucleotide second messenger signaling in bacteria.microLife · 2023Review
- Local signaling enhances output specificity of bacterial c-di-GMP signaling networks.microLife · 2023Review
- Putative nucleotide-based second messengers in archaea.microLife · 2023Review
- Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
The HD-GYP domain, named after two of its conserved sequence motifs, was first described in 1999 as a specialized version of the widespread HD phosphohydrolase domain that had additional highly conserved amino acid residues. Domain associations of HD-GYP indicated its involvement in bacterial signal transduction and distribution patterns of this domain suggested that it could serve as a hydrolase of the bacterial second messenger c-di-GMP, in addition to or instead of the EAL domain. Subsequent studies confirmed the ability of various HD-GYP domains to hydrolyze c-di-GMP to linear pGpG and/or GMP. Certain HD-GYP-containing proteins hydrolyze another second messenger, cGAMP, and some HD-GYP domains participate in regulatory protein-protein interactions. The recently solved structures of HD-GYP domains from four distinct organisms clarified the mechanisms of c-di-GMP binding and metal-assisted hydrolysis. However, the HD-GYP domain is poorly represented in public domain databases, which causes certain confusion about its phylogenetic distribution, functions, and domain architectures. Here, we present a refined sequence model for the HD-GYP domain and describe the roles of its most conserved residues in metal and/or substrate binding. We also calculate the numbers of HD-GYPs encoded in various genomes and list the most common domain combinations involving HD-GYP, such as the RpfG (REC-HD-GYP), Bd1817 (DUF3391-HD-GYP), and PmGH (GAF-HD-GYP) protein families. We also provide the descriptions of six HD-GYP-associated domains, including four novel integral membrane sensor domains. This work is expected to stimulate studies of diverse HD-GYP-containing proteins, their N-terminal sensor domains and the signals to which they respond.
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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.