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Literature summary for 2.7.7.65 extracted from
- Structural and enzymatic characterization of a cAMP-dependent diguanylate cyclase from pathogenic Leptospira species (2017), J. Mol. Biol., 429, 2337-2352 .
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| cAMP | required, Lcd1 DGC activity is negligible in the absence of cAMP and is significantly enhanced in its presence. The GAF domain binds specifically cAMP and has an important role in the regulation of the DGC activity of the GGDEF domain. cAMP binding site and specificity, overview | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |  |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| cloning and expression of gene LIC13137 (Lcd1), gene fragment LIC13137GAF1-175 (Lcd1GAF), and gene fragment LIC13137GAF1-180 as His-tagged proteins in Escherichia coli strain BL21(DE3)RP | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| purified Lcd1GAF domain in complex with cAMP, sitting drop method, mixing 0.0015 ml of 8 mg/ml protein with 4 mM of cAMP and 0.0015 ml of 0.2 M sodium citrate and 20% w/v PEG 3350, 2-4 weeks at 18°C, X-ray diffraction structure determination and analysis at 2.15 A resolution, modelling | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 2 GTP | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 | - |
2 diphosphate + cyclic di-3',5'-guanylate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 | Q72MQ6 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant His-tagged Lcd1, His-tagged Lcd1GAF domain, and His-tagged Lcd1GAF1-180 domain fragment from Escherichia coli strain BL21(DE3)RP by nickel affinity chromatography and gel filtration | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 2 GTP | - |
Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 | 2 diphosphate + cyclic di-3',5'-guanylate | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| dimer | 2 * 37600, apoform Lcd1GAF domain, SDS-PAGE, 2 * 37700, Lcd1GAF domain in complex with cAMP, SDS-PAGE | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
| More | enzyme Lcd1 has an N-terminal cGMP-specific phosphodiesterase domain, an adenylyl cyclase domain, a FhlA (GAF) domain, and a C-terminal GGDEF domain. The N-terminal GAF domain comprises residues 28-165 and the C-terminal GGDEF domain residues 178-326, with a predicted linker (residues 166-177) between them. The full-length Lcd1 and its GAF domain form dimers in solution. The dimer interface involves 48 residues, mainly from alpha1 and alpha6. The dimerization interface involves many hydrogen bonds. On their own, these intermolecular H-bonds can be replaced with protein-solvent hydrogen bonds with little energetic penalty if it is not for additional intersubunit interactions involving hydrophobic and aromatic residues I11, Y14, L25, V152, F160, I162, H167, and Y171. In the full-length protein, the C-terminus of the GAF domain is linked to the N-terminus of the GGDEF domain. In the Lcd1GAF-cAMP dimer, the two C-terminal alpha6 helices are pointing in the same direction, and the Calpha atoms of the C-terminal T174 residues are separated by only 6.4 A | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| cAMP-dependent diguanylate cyclase | - |
Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
| cGMP-specific phosphodiesterase | UniProt | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
| DGC | - |
Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
| Lcd1 | - |
Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
| LIC13137 | - |
Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
| LIC_13137 | - |
Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 30 | - |
assay at | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
Temperature Stability [°C]
| Temperature Stability Minimum [°C] | Temperature Stability Maximum [°C] | Comment | Organism |
|---|---|---|---|
| additional information | - |
the addition of cAMP increases the thermal stability of Lcd1GAF_1-180 by 7°C, while cGMP and c-di-GMP do not significantly alter the protein's thermal stability | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
| 52 | - |
Tm of apo-Lcd1GAF domain and of c-di-GMP-bound Lcd1GAF domain | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
| 52.5 | - |
Tm of cGMP-bound Lcd1GAF domain | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
| 59 | - |
Tm of cAMP-bound Lcd1GAF domain | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.13 | - |
GTP | in presence of cAMP, pH 8.0, 30°C | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 8 | - |
assay at | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | close LIC13137 orthologues, with more than 23% identity, are exclusively found in pathogenic species of the Leptospira genus | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
| additional information | enzyme Lcd1 has an N-terminal cGMP-specific phosphodiesterase domain, an adenylyl cyclase domain, a FhlA (GAF) domain, and a C-terminal GGDEF domain. The GAF domain regulates the DGC activity of Lcd1. The GAF domain binds specifically cAMP and has animportant role in the regulation of the DGC activity of the GGDEF domain. Lcd1 DGC activity is negligible in the absence of cAMP and is significantly enhanced in its presence. Structure comparison, overview | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
| physiological function | enzyme Lcd1 is a potential node for the integration of cAMP and c-di-GMP signaling in Leptospira interrogans | Leptospira interrogans serogroup Icterohaemorrhagiae serovar copenhageni Fiocruz L1-130 |
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