User:Sarasunadalkilic/sandbox

Original – Response Regulator

Classification
Response regulators can be divided into at least three broad classes:
 * Single-domain response regulators, which contain only a receiver domain and which use protein-protein interactions to exert their downstream biological effects; for example, the chemotaxis regulator CheY.
 * Response regulators with a DNA-binding effector domain, usually of helix-turn-helix architecture.
 * Response regulators with effector domains that have enzymatic functions, giving rise to secondary messenger molecules such as cAMP.

More comprehensive classifications based on more detailed analysis of domain architecture are possible, and find that response regulators with DNA-binding domains are by far the most common.

Edit – Response Regulator

Classification
Response regulators can be divided into at least three broad classes, based on the features of effector domains: regulators with a DNA-binding effector domain, regulators with an enzymatic effector domain, and single-domain response regulators. More comprehensive classifications based on more detailed analysis of domain architecture are possible. Beyond these broad categorizations, there are response regulators with other types of effector domains, including RNA-binding effector domains.

Regulators with a DNA-binding effector domain are the most common response regulators, and have direct impacts on transcription. They tend to interact with their cognate regulators at an N-terminus receiver domain, and contain the DNA-binding effector towards the C-terminus. Once phosphorylated at the receiver domain, the response regulator dimerizes, gains enhanced DNA binding capacity and acts as a transcription factor. The architecture of DNA binding domains are characterized as being variations on helix-turn-helix motifs. One variation, found on the response regulator OmpR of the EnvZ/OmpR two-component system and other OmpR-like response regulators, is a "winged helix" architecture. OmpR-like response regulators are the largest group of response regulators and the winged helix motif is widespread. Other subtypes of DNA-binding response regulators include FixJ-like and NtrC-like regulators. DNA-binding response regulators are involved in various uptake processes, including nitrate/nitrite (NarL, found in most prokaryotes).

The second class of multidomain response regulators are those with enzymatic effector domains. These response regulators can participate in signal transduction, and generate secondary messenger molecules. Examples include the chemotaxis regulator CheB, with a methylesterase domain that is inhibited when the response regulator is in the inactive unphosphorylated conformation. Other enzymatic response regulators include c-di-GMP phosphodiesterases (e.g. VieA in V. cholerae), protein phosphatases and histidine kinases.

A relatively small number of response regulators, single-domain response regulators, only contain a receiver domain, relying on protein-protein interactions to exert their downstream biological effects. The receiver domain undergoes a conformational change as it interacts with an autophosphorylated histidine kinase, and consequently the response regulator can initiate further reactions along a signaling cascade. Prominent examples include the chemotaxis regulator CheY, which interacts with flagellar motor proteins directly in its phosphorylated state.

Sequencing has so far shown that the distinct classes of response regulators are unevenly distributed throughout various taxa, including across domains. While response regulators with DNA-binding domains are the most common in bacteria, single-domain response regulators are more common in archaea, with other major classes of response regulators seemingly absent from archaeal genomes.

--Sarasunadalkilic (talk) 06:03, 8 October 2017 (UTC)