Table I.
Representative High-Resolution Structures of c-di-GMP Metabolizing Enzymes and Protein Receptors
| Protein | Organism | Function | Conserved domains | PDB code and nucleotide-bound state | References |
|---|---|---|---|---|---|
| C-di-GMP turnover enzymes | |||||
| Diguanylate cyclases | |||||
| PleD | Caulobacter crescentus | C-di-GMP synthesis; polar differentiation | Two CheY-like REC domains; | 1W25 (c-di-GMP/Mg complex); | 41,44 |
| GGDEF domain | 2WB4 (c-di-GMP/ Mg/BeF3 complex); | ||||
| 2V0N (c-di-GMP/Mg/BeF3/ GTP-α-S complex) | |||||
| WspR | Pseudomonas aeruginosa | C-di-GMP synthesis; biofilm formation and persistence | CheY-like REC domain; | 3BRE (c-di-GMP/Mg complex); | 39,45 |
| GGDEF domain | 3I5B (GGDEF domain; apoprotein) | ||||
| Phosphodiesterases | |||||
| YkuI | Bacillus subtilis | C-di-GMP hydrolysis | EAL domain; | 2BAS (apoprotein) | 46 |
| PAS-like domain | 2W27 (c-di-GMP/Ca complex) | ||||
| BlrP1 | Klebsiella pneumoniae | Light-regulated c-di-GMP hydrolysis | BLUF sensor domain; | 3GFX 3GG1 (c-di-GMP/ Ca/FMN complex); | 47 |
| EAL domain | 3GFY (c-di-GMP/FMN complex); | ||||
| 3GFZ, 3GG0 (c-di-GMP/ Mn/FMN complex) | |||||
| Bd1817 | Bdellovibrio bacteriovorus | Unknown | HD-GYP domain | 3TM8, 3TMB, 3TMC, 3TMD (apoprotein) | 48 |
| C-di-GMP protein receptors | |||||
| PilZ domain proteins | |||||
| VCA0042/PlzD | Vibrio cholerae | Potential role in virulence | YcgR-N* domain; | 1YLN (apoprotein); | 28 |
| PilZ domain | 2RDE (c-di-GMP complex) | ||||
| PP4397 | Pseudomonas putida | unknown | YcgR-N* domain; | 3KYF (c-di-GMP complex) | 31 |
| PilZ domain | |||||
| PA4608 | Pseudomonas aeruginosa | Potential role in biofilm formation and/or quorum sensing | PilZ domain | 1YWU (apoprotein); | 30,32 |
| 2L74 (c-di-GMP complex) | |||||
| Transcription factors | |||||
| VpsT | Vibrio cholerae | Global transcription control; biofilm formation | Noncanonical REC domain; | 3KLN (apoprotein); | 37 |
| HTH DNA-binding domain | 3KLO (c-di-GMP complex) | ||||
| Clp | Xanthomonas campestris | Global transcription control; virulence | cNMP-binding domain; | 3IWZ (apoprotein) | 40 |
| HTH DNA-binding domain | |||||
| Degenerate EAL domains | |||||
| FimX | Pseudomonas aeruginosa | Type IV pilus-mediated twitching motility | CheY-like REC domain; | 3HV9 (EAL domain; apoprotein); | 35 |
| PAS domain; GGDEF domain; EAL domain | 3HV8 (EAL domain; c-di-GMP complex); | ||||
| 3HVA (GGDEF domain); | |||||
| 3HVB (GGDEF-EAL module; apoprotein) | |||||
| LapD | Pseudomonas fluorescens | Adhesin maintenance; biofilm formation and dispersal | Periplasmic output domain; | 3PJV (periplasmic domain); | 49 |
| HAMP domain; GGDEF domain; EAL domain | 3PJT, 3PJU (EAL domain; c-di-GMP complex); | ||||
| 3PJW, 3PJX (GGDEF-EAL module; apoprotein) | |||||
| Others | |||||
| PNPase | Escherichia coli | O2-dependent RNA degradation | Two RNase PH domains; | 3CDI (apoprotein); | 50 |
| KH RNA-binding domain; | 3CDJ (PH1-PH2 module; apoprotein) | ||||
| S1 RNA-binding domain | |||||
Conserved domains responsible for c-di-GMP synthesis, degradation, or recognition are underlined.