Adenylyl cyclase
Adenylyl cyclase (, also commonly known as adenyl cyclase and adenylate cyclase, abbreviated AC) is an enzyme with key regulatory roles in essentially all cells. It is the most polyphyletic known enzyme: six distinct classes have been described, all catalyzing the same reaction but representing unrelated gene families with no known sequence or structural homology. The best known class of adenylyl cyclases is class III or AC-III (Roman numerals are used for classes). AC-III occurs widely in eukaryotes and has important roles in many human tissues. All classes of adenylyl cyclase catalyse the conversion of adenosine triphosphate  (ATP) to 3',5'-cyclic AMP (cAMP) and pyrophosphate. Magnesium ions are generally required and appear to be closely involved in the enzymatic mechanism. The cAMP produced by AC then serves as a regulatory signal via specific cAMP-binding proteins, either transcription factors, enzymes (e.g., cAMP-dependent kinases), or ion transporters. Classes. Class I. The first class of adenylyl cyclases occur in many bacteria including "E. coli" (as CyaA [unrelated to the Class II enzyme]). This was the first class of AC to be characterized. It was observed that "E. coli" deprived of glucose produce cAMP that serves as an internal signal  to activate expression of genes for importing and metabolizing other sugars. cAMP exerts this effect by binding the transcription factor CRP, also known as CAP. Class I AC's are large cytosolic enzymes (~100 kDa) with a large regulatory domain (~50 kDa) that indirectly senses glucose levels. , no crystal structure is available for class I AC. Some indirect structural information is available for this class. It is known that the N-terminal half is the catalytic portion, and that it requires two Mg ions. S103, S113, D114, D116 and W118 are the five absolutely essential residues. The class I catalytic  domain () belongs to the same superfamily () as the palm domain of DNA polymerase beta (). Aligning its sequence onto the structure onto a related archaeal CCA tRNA nucleotidyltransferase () allows for assignment of the residues to specific functions: γ-phosphate binding, structural stabilization, DxD motif for metal ion binding, and finally ribose binding. Class II. These adenylyl cyclases are toxins secreted by pathogenic bacteria such as "Bacillus anthracis", "Bordetella pertussis", "Pseudomonas aeruginosa", and "Vibrio vulnificus" during infections. These bacteria also secrete proteins that enable the AC-II to enter host cells, where the exogenous AC activity undermines normal cellular processes. The genes  for Class II ACs are known as cyaA, one of which is anthrax toxin. Several crystal structures are known for AC-II enzymes. Class III. These adenylyl cyclases are the most familiar based on extensive study due to their important roles in human health. They are also found in some bacteria, notably "Mycobacterium tuberculosis" where they appear to have a key role in pathogenesis. Most AC-III's are integral membrane proteins involved in transducing extracellular signals into intracellular responses. A Nobel Prize was awarded to Earl Sutherland in 1971 for discovering the key role of AC-III in human  liver, where adrenaline indirectly stimulates AC to mobilize stored energy in the "fight or flight" response. The effect of adrenaline is via a G protein signaling cascade, which transmits chemical signals from outside the cell across the membrane to the inside of the cell (cytoplasm). The outside signal (in this case, adrenaline) binds to a receptor, which transmits a signal to the G protein, which transmits a signal to adenylyl cyclase, which transmits a signal by converting adenosine triphosphate to cyclic adenosine monophosphate (cAMP). cAMP is known as a second messenger. Cyclic AMP is an important molecule in eukaryotic signal  transduction, a so-called second messenger. Adenylyl cyclases are often activated or inhibited by G proteins, which are coupled to membrane receptors and thus can respond to hormonal or other stimuli. Following activation of adenylyl cyclase, the resulting cAMP acts as a second messenger by interacting with and regulating other proteins such as protein kinase A and cyclic nucleotide-gated ion channels. Photoactivated adenylyl cyclase (PAC) was discovered in "Euglena gracilis" and can be expressed in other organisms through genetic manipulation. Shining blue light on a cell containing PAC activates it and abruptly increases the rate of conversion of ATP  to cAMP. This is a useful technique for researchers in neuroscience because it allows them to quickly increase the intracellular cAMP levels in particular neurons, and to study the effect of that increase in neural activity on the behavior of the organism. A green-light activated rhodopsin adenylyl cyclase (CaRhAC) has recently been engineered by modifying the nuclecotide binding pocket of rhodopsin guanylyl cyclase. Structure. Most class III adenylyl cyclases are transmembrane proteins with 12 transmembrane segments. The protein is organized with 6 transmembrane segments, then the C1 cytoplasmic domain, then another 6 membrane segments, and then a second cytoplasmic  domain called C2. The important parts for function are the N-terminus and the C1 and C2 regions. The C1a and C2a subdomains are homologous and form an intramolecular 'dimer' that forms the active site. In "Mycobacterium tuberculosis" and many other bacterial cases, the AC-III polypeptide is only half as long, comprising one 6-transmembrane domain followed by a cytoplasmic domain, but two of these form a functional homodimer that resembles the mammalian architecture with two active sites. In non-animal class III ACs, the catalytic cytoplasmic domain is seen associated with other (not necessarily transmembrane) domains. Class III  adenylyl cyclase domains can be further divided into four subfamilies, termed class IIIa through IIId. Animal membrane-bound ACs belong to class IIIa. Mechanism. The reaction happens with two metal cofactors (Mg or Mn) coordinated to the two aspartate residues on C1. They perform a nucleophilic attack of the 3'-OH group of the ribose on the α-phosphoryl group of ATP. The two lysine and aspartate residues on C2 selects ATP over GTP for the substrate, so that the enzyme is not a guanylyl cyclase. A pair of arginine and asparagine residues on C2 stabilizes the transition state. In many  proteins, these residues are nevertheless mutated while retaining the adenylyl cyclase activity. Types. There are ten known isoforms of adenylyl cyclases in mammals: These are also sometimes called simply AC1, AC2, etc., and, somewhat confusingly, sometimes Roman numerals are used for these isoforms that all belong to the overall AC class III. They differ mainly in how they are regulated, and are differentially expressed in various tissues throughout mammalian development. Regulation. Adenylyl cyclase is regulated by G proteins, which can be found in the monomeric form or the heterotrimeric form, consisting of three subunits. Adenylyl cyclase activity is controlled by  heterotrimeric G proteins. The inactive or inhibitory form exists when the complex consists of alpha, beta, and gamma subunits, with GDP bound to the alpha subunit. In order to become active, a ligand must bind to the receptor and cause a conformational change. This conformational change causes the alpha subunit to dissociate from the complex and become bound to GTP. This G-alpha-GTP complex then binds to adenylyl cyclase and causes activation and the release of cAMP. Since a good signal requires the help of enzymes, which turn on and off signals quickly, there must also be a mechanism  in which adenylyl cyclase deactivates and inhibits cAMP. The deactivation of the active G-alpha-GTP complex is accomplished rapidly by GTP hydrolysis due to the reaction being catalyzed by the intrinsic enzymatic activity of GTPase located in the alpha subunit. It is also regulated by forskolin, as well as other isoform-specific effectors: In neurons, calcium-sensitive adenylyl cyclases are located next to calcium ion channels for faster reaction to Ca influx; they are suspected of playing an important role in learning processes. This is supported by the fact that adenylyl cyclases are "coincidence detectors", meaning that they are  activated only by several different signals occurring together. In peripheral cells and tissues adenylyl cyclases appear to form molecular complexes with specific receptors and other signaling proteins in an isoform-specific manner. Function. Adenylyl cyclase has been implicated in memory formation, functioning as a coincidence detector. Class IV. AC-IV was first reported in the bacterium "Aeromonas hydrophila", and the structure of the AC-IV from "Yersinia pestis" has been reported. These are the smallest of the AC enzyme classes; the AC-IV (CyaB) from "Yersinia" is a dimer of 19 kDa subunits with no known regulatory components (). AC-IV  forms a superfamily with mamallian thiamine-triphosphatase called CYTH (CyaB, thiamine triphosphatase). Classes V and VI. These forms of AC have been reported in specific bacteria ("Prevotella ruminicola" and "Rhizobium etli" , respectively) and have not been extensively characterized. There are a few extra members (~400 in Pfam) known to be in class VI. Class VI enzymes possess a catalytic core similar to the one in Class III.