From Proteopedia

DgcZ from E. coli

Zn Binding Site DgcZ. The Cys52 reside is not the N-terminal residue, but the rest of the 𝝰helix 2 was not successfully crystallized.

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 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

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.

Catalytic GGEEF Domain

The GGEEF domain of DgcZ is part of the GGDEF family of proteins that includes a conserved sequence, GG[DE][DE]F[2].The GGEEF domain is a homodimer consisting of a central five-stranded β-sheet surrounded by five α-helices. Each dimer contains an active half-site that, when combined together in a productive conformation, form the entire active site. Each half-site binds one GTP molecule. The guanyl base forms hydrogen bonds with Asp-173 and Asn-182 to hold it in the active site. A Mg²⁺ ion stabilizes the negative charges on the phosphate groups. When in the productive conformation, each GTP is held in close proximity with the α-phosphate groups overlapping C3 of the ribose. This conformation allows the α-phospate of one GTP to react with the alcohol group on C3 of the ribose of the other GTP, resulting in a cyclization of the two molecules into c-di-GMP. The ribose of each guanosine triphosphate, and subsequent product c-di-GMP riboses, are held only loosely by the enzyme, while the phosphate groups are not bound at all.

Mechanism of Action

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.

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

3. The β and γ phosphates of GTP are kicked off to form c-di-GMP.

CZB Domain

The CZB domain is responsible for regulating the function of DgcZ. The domain contains the allosteric binding site of the enzyme with cooperative binding. Four residues bind zinc with a high affinity even at 10^-16M concentrations. Due to the tightness of Zinc binding, the enzyme has not yet been crystallized in the active conformation without the presence of Zinc metal inhibitor.

Zn Coordination to amino acid residues on three of the four 𝝰 helices of DgcZ

Zinc Binding Site

Most cells possess efficient Zinc uptake systems, as Zinc is a reactive Lewis Acid. Zinc binds incredibly tightly to this enzyme at subfemtomolar concentrations. The Zinc co-purified with the protein.Zinc allosterically inhibits the activity of enzyme DgcZ through two allosteric binding sites located on the CZB domain. The inhibition prevents regulation of GGDEF domain function, the location of the active site. The CZB domain is folded into four anti-parallel α-helices as a 2-fold symmetric homodimer, with the N-terminus on the helix 𝝰4. The allosteric binding site includes amino acids, H22 of 𝝰1, C52 of 𝝰2, and H79 and H83 of 𝝰3, that span three of the four alpha helices of the CZB domain coordinating the Zinc residue in a tetrahedral fashion. Zahringer et al. mutated Cys52 to Ala through site-directed mutagenesis, resulting in a lack of coordination on α2. The cysteine residue is not essential for Zinc binding, as Zinc still coordinates to the three His residues with the Cys52Ala mutation, but α2 is free to move and expose the Zinc binding pocket. This exposure was found to lower the protein's affinity for zinc, as the mutation of cysteine to alanine increased the activity of the DgcZ. Using EDTA, Zinc can be removed from the CZB domain. The zinc has higher affinity for EDTA than CZB when EDTA concentration is higher than the concentration of DgcZ. When not coordinated to zinc, the CZB domain adopts a conformation that straightens the 𝝰1 helix shifts, shifting hydrophobic residues on the α-helices into the center and the GGEEF domain into its productive conformation, increasing activity of DgcZ. Activity increases without Zinc due to activation of poly-GlcNAc production and biofilm formation, and maximal cyclic di-GMP production.

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References

<Jenny Draper, K. Karplus, K. Ottemann. Identification of a Chemoreceptor Zinc-Binding Domain Common to Cytoplasmic Bacterial Chemoreceptors. Journal of Bacteriology. Vol. 193, No. 17. 4338-4345. (2011).> <Carmen Chan, R. Paul, D. Samoray, N. Amiot, B. Giese, U. Jenal, T. Schirmer. Structural basis of activity and allosteric control of diguanylate cyclases. PNAS. Vol 101. No. 49 17084-17089. (2004).>