Sandbox Reserved 1070: Difference between revisions

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== 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 [https://en.wikipedia.org/wiki/Chemotaxis chemotaxis]~~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 [https://en.wikipedia.org/wiki/Chemotaxis 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.

===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.

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 ~~Mg2~~+ ions.

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 Mg2+ ions.

2. The deprotonated Oxygen then acts as a nucleophile to attack the 𝝰phosphate of GTP.

Sandbox Reserved 1070: Difference between revisions

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@@ Line 8: / Line 8: @@
 == 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 <span class="plainlinks">[https://en.wikipedia.org/wiki/Chemotaxis chemotaxis]</span>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===
@@ Line 16: / Line 16: @@
 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.
-. 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 Mg2+ ions.
+. 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.
 . The deprotonated Oxygen then acts as a nucleophile to attack the 𝝰phosphate of GTP.