Sandbox Reserved 1070: Difference between revisions
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== Biological Function == | == Biological Function == | ||
Diguanylate cyclases, class 2 transferase enzymes, catalyze the production of cyclic dimeric-guanosine monophosphate (c-di-GMP), important to signal transduction as a second messenger. Signal transduction is the process of sending signals through cells to promote responses most commonly through phosphorylation or dephosphorylation events. Enzyme DgcZ from ''E. coli'' acts a catalyst to synthesize cyclic di-GMP from two substrate guanosine triphosphate (GTP) molecules to aid in communication of signals throughout the bacteria. C-di-GMP is a second messenger in the production of poly-β-1,6-N-acetylglucosamine (poly-GlcNAc), a polysaccharide required for ''E. coli'' biofilm production. This biofilm allows ''E. coli'' to adhere to extracellular surfaces. The DgcZ protein | Diguanylate cyclases, class 2 transferase enzymes, catalyze the production of cyclic dimeric-guanosine monophosphate (c-di-GMP), important to signal transduction as a second messenger. Signal transduction is the process of sending signals through cells to promote responses most commonly through phosphorylation or dephosphorylation events. Enzyme DgcZ from ''E. coli'' acts a catalyst to synthesize cyclic di-GMP from two substrate guanosine triphosphate (GTP) molecules to aid in communication of signals throughout the bacteria. C-di-GMP is a second messenger in the production of poly-β-1,6-N-acetylglucosamine (poly-GlcNAc), a polysaccharide required for ''E. coli'' biofilm production. This biofilm allows ''E. coli'' to adhere to extracellular surfaces. The DgcZ protein has C2 symmetry composed of two domains: the catalytic glycine-glycine-glutamate-glutamate-phenylalanine (GGEEF) domain responsible for synthesizing c-di-GMP and the regulatory chemoreceptor zinc binding (CZB) domain comprising two zinc binding sites. DgcZ binds zinc with sub-femtomolar affinity. When zinc is bound, the CZB and GGEEF domains adopt conformations that inhibit DgcZ function. | ||
== Structural Overview == | == Structural Overview == | ||
Enzyme DgcZ has been co-crystallized with Zinc conforming it to its inactivated conformation. The CZB domain is common to many bacterial lineages, appearing most commonly in bacterial chemoreceptors involved in chemotaxis. The second most common group of CZB domains is that of DgcZ homologs. [1]. The domain has an important role in signal transduction of bacteria[1]. 30 small bacterial proteins of family PRK0984 from differing strands of ''E. coli'' contain a CZB domain N-terminal to a GGDEF domain[1]. The GGEEF domain of DgcZ is common to this family of enzymes containing the GGDEF domain. ''E. coli'' DgcZ is a protein made of two domains each of which is a symmetric homodimer. The GGEEF domain is catalytic in that it contains the active sites used for cyclizing GTP into c-di-GMP. The CZB domain is used for ligand-mediated regulation of c-di-GMP production. Zinc binds as an allosteric inhibitor in coordination with four residues to shift the protein into an inactive conformation. | Enzyme DgcZ has been co-crystallized with Zinc conforming it to its inactivated conformation. The CZB domain is common to many bacterial lineages, appearing most commonly in bacterial chemoreceptors involved in <span class="plainlinks">[https://en.wikipedia.org/wiki/Chemotaxis chemotaxis]</span>. The second most common group of CZB domains is that of DgcZ homologs. [1]. The domain has an important role in signal transduction of bacteria[1]. 30 small bacterial proteins of family PRK0984 from differing strands of ''E. coli'' contain a CZB domain N-terminal to a GGDEF domain[1]. The GGEEF domain of DgcZ is common to this family of enzymes containing the GGDEF domain. ''E. coli'' DgcZ is a protein made of two domains each of which is a symmetric homodimer. The GGEEF domain is catalytic in that it contains the active sites used for cyclizing GTP into c-di-GMP. The CZB domain is used for ligand-mediated regulation of c-di-GMP production. Zinc binds as an allosteric inhibitor in coordination with four residues to shift the protein into an inactive conformation. | ||
===Catalytic GGEEF Domain=== | ===Catalytic GGEEF Domain=== | ||
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Diguanylate cyclases only function efficiently as dimers, to bind both GGDEF domains holding the substrates. The presence of Zinc disrupts the ability of the two domains to overlap. | Diguanylate cyclases only function efficiently as dimers, to bind both GGDEF domains holding the substrates. The presence of Zinc disrupts the ability of the two domains to overlap. | ||
1. The enzyme coordinates the substrate GTP to allow for deprotonation of the C3 -OH groups of the ribose. The negatively charged Oxygens on the phosphate groups of GTP are stabilized by | 1. The enzyme coordinates the substrate GTP to allow for deprotonation of the C3 -OH groups of the ribose. The negatively charged Oxygens on the phosphate groups of GTP are stabilized by Mg<sup>2+</sup> ions. | ||
2. The deprotonated Oxygen then acts as a nucleophile to attack the 𝝰phosphate of GTP. | 2. The deprotonated Oxygen then acts as a nucleophile to attack the 𝝰phosphate of GTP. | ||
