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Synonyms
diguanylate cyclase, tlr0924, vc0395_0300, pa3177, all2874, pa0847, slr1143, pa4367, ggdef domain-containing protein, xac0610,
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2 GTP
2 diphosphate + cyclic di-3',5'-guanylate
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GTP + GTP
cyclic di-3',5'-guanylate + diphosphate + diphosphate
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analyses by pyrophosphatase-coupled spectrophotometric assay
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GTP + GTP
cyclic-di-3',5'-GMP + diphosphate + diphosphate
pH 7.8
reaction stop with 25 mM EDTA, pH 6, KD (cyclic-di-3,5-GMP): 0.3 microM or 0.4 microM (in presence of activator BeF3)
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2 GTP
2 diphosphate + cyclic di-3',5'-guanylate
GTP
cyclic di-3',5'-guanylate + diphosphate
additional information
?
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2 GTP
2 diphosphate + cyclic di-3',5'-guanylate
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2 GTP
2 diphosphate + cyclic di-3',5'-guanylate
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2 GTP
2 diphosphate + cyclic di-3',5'-guanylate
the enzyme uses its GGDEF domain for catalysis. The DgcP of Caulobacter crescentus binds dimeric c-di-GMP at an allosteric site I-site that is characterized by the RxxD motif. Binding of cyclic-di-GMP at the I-site accounts for a strong non-competitive product inhibition, which establishes a limit on the cellular c-di-GMP concentration
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GTP
cyclic di-3',5'-guanylate + diphosphate
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GTP
cyclic di-3',5'-guanylate + diphosphate
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GTP
cyclic di-3',5'-guanylate + diphosphate
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GTP
cyclic di-3',5'-guanylate + diphosphate
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diguanylate cyclase activity constitutes the signaling output of the PleD response regulator
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additional information
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mode of GTPalphaS/Mg2+-binding suggests two-metal catalytic mechanism analogous to adenylate cyclases
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additional information
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mode of GTPalphaS/Mg2+-binding suggests two-metal catalytic mechanism analogous to adenylate cyclases
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additional information
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on-rates constants of substrate and product range between 100/sec and 300/sec
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additional information
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on-rates constants of substrate and product range between 100/sec and 300/sec
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additional information
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analysis of the DGC specificity, overview
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2-(5-amino-1,3,4-thiadiazol-2-yl)-N'-[(1E,2E)-3-(3-nitrophenyl)prop-2-en-1-ylidene]acetohydrazide
4% inhibition at 0.1 mM
3-(3,5-dioxo-2,3,4,5-tetrahydro-1,2,4-triazin-6-yl)-N'-[(E)-(4-nitrophenyl)methylidene]propanehydrazide
11.0% inhibition at 0.1 mM
3-nitro-N'-[(E)-(2,3,4-trihydroxyphenyl)methylidene]benzene-1-sulfonohydrazide
85% inhibition at 0.1 mM, competitive binding
cyclic di-3',5'-guanylate
noncompetitive product inhibition, binding causes crosslinking of diguanylate cyclase (GGDEF) domains within the dimer, integrity of only one inhibitory site required for inhibition
cyclic-di-3',5'-GMP
allosteric feedback, product inhibition, independent of activation status, binding induces change in conformation and protein-solvent interactions
N'-[(E)-(2,4-dihydroxyphenyl)methylidene]-4-methyl-3-nitrobenzene-1-sulfonohydrazide
N'-[(E)-(2-hydroxyphenyl)methylidene]-4-methyl-3-nitrobenzene-1-sulfonohydrazide
13% inhibition at 0.1 mM
N'-[(E)-(3,4-dihydroxyphenyl)methylidene]-4-methyl-3-nitrobenzene-1-sulfonohydrazide
83.4% inhibition at 0.1 mM, competitive binding
2',3'-O-[4-(dihydroxyiminio)-2,6-dinitrocyclohexa-2,5-diene-1,1-diyl]guanosine 5'-triphosphate
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2'-O-[2-(methylamino)benzoyl]guanosine 5'-(gammaS)triphosphate
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2'-O-[2-(methylamino)benzoyl]guanosine 5'-triphosphate
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2-hydroxy-5-[(E)-[4-[(pyridin-2-yl)sulfamoyl]phenyl]diazenyl]benzoic acid
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3-O-alpha-L-rhamnopyranosyl-(1->2)-beta-D-galactopyranosyl-(1->2)-beta-D-glucuronopyranosyl soyasapogenol B 22-O-alpha-D-glucopyranoside
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4-(2,5-dimethylphenoxy)-N-(4-morpholin-4-ylphenyl)butanamide
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4-chloro-3-nitro-N'-[(E)-(2,3,4-trihydroxyphenyl)methylidene]benzene-1-sulfonohydrazide
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9-(3-[4-[(2-amino-6-chloro-9H-purin-9-yl)methyl]-1H-1,2,3-triazol-1-yl]propyl)-6-chloro-9H-purin-2-amine
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cyclic 3',5'-diguanylate
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product inhibition is due to domain immobilization and sets an upper limit for the concentration of this second messenger in the cell
cyclic di-3',5'-(2'-fluoroguanylate)
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cyclic di-3',5'-guanlylate
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strong product inhibition
cyclic di-3',5'-guanylate
cyclic di-3',5'-inosinylic acid
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cyclic diguanylate
noncompetitive, product inhibition
KCl
25 mM, slight decrease in activity
N'-((1E)-(4-ethoxy-3-[(8-oxo-1,5,6,8-tetrahydro-2H-1,5-methanopyrido[1,2-a][1,5]diazocin-3(4H)-yl)methylphenyl)methylene)]-3,4,5-trihydroxybenzohydrazide
LP3134
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N'-[(E)-(3,4-dihydroxyphenyl)methylidene]-4-methyl-3-nitrobenzene-1-sulfonohydrazide
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N-(4-anilinophenyl)benzamide
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NaCl
activity decreases with increasing concentrations of NaCl
[2- oxo-2-(2-oxopyrrolidin-1-yl)ethyl] 1,3-benzothiazole-6-carboxylate
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N'-[(E)-(2,4-dihydroxyphenyl)methylidene]-4-methyl-3-nitrobenzene-1-sulfonohydrazide
6% inhibition at 0.1 mM
N'-[(E)-(2,4-dihydroxyphenyl)methylidene]-4-methyl-3-nitrobenzene-1-sulfonohydrazide
17% inhibition at 0.1 mM
cyclic di-3',5'-guanylate
noncompetitive product inhibition at an allosteric binding site fully contained within the GGDEF domain. Core of the binding site is an RXXD motif formed by residues R359, D362, and R390
cyclic di-3',5'-guanylate
product inhibition, allosteric feedback regualtion is not affected by the activation state of enzyme
additional information
virtual screening of the ZINC database, in silico discovery and in vitro validation of catechol-containing sulfonohydrazide compounds as potent inhibitors of the diguanylate cyclase PleD. The compounds retrieved from the pharmacophore searches are docked into the active site of PleD, by means of Molegro Virtual Docker (MVD) software (CLCbio), using the three-dimensional structure of PleD (PDB ID 2V0N). Binding of N'-[(E)-(3,4-dihydroxyphenyl)methylidene]-4-methyl-3-nitrobenzene-1-sulfonohydrazide and 3-nitro-N'-[(E)-(2,3,4-trihydroxyphenyl)methylidene]benzene-1-sulfonohydrazide to PleD is stabilized by polar interactions with residues surrounding the GTP binding pocket, namely, N335, D344, and R366. N'-[(E)-(3,4-dihydroxyphenyl)methylidene]-4-methyl-3-nitrobenzene-1-sulfonohydrazide and 3-nitro-N'-[(E)-(2,3,4-trihydroxyphenyl)methylidene]benzene-1-sulfonohydrazide share a hydrazine moiety with the previously identified inhibitors LP3134 and LP4010, which has been predicted to interact with the amino group of N335
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additional information
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virtual screening of the ZINC database, in silico discovery and in vitro validation of catechol-containing sulfonohydrazide compounds as potent inhibitors of the diguanylate cyclase PleD. The compounds retrieved from the pharmacophore searches are docked into the active site of PleD, by means of Molegro Virtual Docker (MVD) software (CLCbio), using the three-dimensional structure of PleD (PDB ID 2V0N). Binding of N'-[(E)-(3,4-dihydroxyphenyl)methylidene]-4-methyl-3-nitrobenzene-1-sulfonohydrazide and 3-nitro-N'-[(E)-(2,3,4-trihydroxyphenyl)methylidene]benzene-1-sulfonohydrazide to PleD is stabilized by polar interactions with residues surrounding the GTP binding pocket, namely, N335, D344, and R366. N'-[(E)-(3,4-dihydroxyphenyl)methylidene]-4-methyl-3-nitrobenzene-1-sulfonohydrazide and 3-nitro-N'-[(E)-(2,3,4-trihydroxyphenyl)methylidene]benzene-1-sulfonohydrazide share a hydrazine moiety with the previously identified inhibitors LP3134 and LP4010, which has been predicted to interact with the amino group of N335
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additional information
screenings for chemicals capable of inhibiting the c-di-GMP synthesis activity of DGCs have been performed in order to inhibit bacterial biofilm formation. 2',3'-O-(2,4,6-trinitrophenyl) (TNP)- and 2' (3')-O-(N-methylanthraniloyl) (MANT)-substituted nucleotides are potent inhibitors of guanylyl and adenylyl cyclases
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additional information
screenings for chemicals capable of inhibiting the c-di-GMP synthesis activity of DGCs have been performed in order to inhibit bacterial biofilm formation. 2',3'-O-(2,4,6-trinitrophenyl) (TNP)- and 2' (3')-O-(N-methylanthraniloyl) (MANT)-substituted nucleotides are potent inhibitors of guanylyl and adenylyl cyclases
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4-(5-[(E)-[2-(4-amino-1,2,5-oxadiazole-3-carbonyl)hydrazinylidene]methyl]furan-2-yl)benzoic acid
18% activation at 0.1 mM
4-chloro-N'-[(E)-(4-cyanophenyl)methylidene]-3-nitrobenzene-1-sulfonohydrazide
15% activation at 0.1 mM
4-[(E)-[2-(4-hydroxy-6-methylpyrimidin-2-yl)hydrazinylidene]methyl]phenyl 3-nitrobenzoate
8% activation at 0.1 mM
4-[(E)-[2-(4-sulfamoylphenyl)hydrazinylidene]methyl]benzoic acid
6% activation at 0.1 mM
N'-[(E)-(4-chloro-3-nitrophenyl)methylidene]-4-methyl-3-nitrobenzene-1-sulfonohydrazide
3% activation at 0.1 mM
N'-[(E)-(4-cyanophenyl)methylidene]-4-methyl-3-nitrobenzene-1-sulfonohydrazide
4% activation at 0.1 mM
beryllium fluoride
BeF3-, pseudo-phosphorylation, enhances dimerisation by lowering KD to less than 10 microM, tightens dimer interface between two D1/D2 domains, modification activates enzyme
beryllium fluoride
BeF3, phosphoryl mimic, optimum concentration: 1 mM BeCl2/10 mM NaF (nonspecifcally inhibitory at higher concentrations), causes dimerisation and cyclic di-3,5-guanylate synthesis, no influence on cyclic-di-GMP binding affinity and thus allosteric regulation
additional information
PleD contains an extra metal binding site or beryllium metal for activation
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additional information
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PleD contains an extra metal binding site or beryllium metal for activation
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0.00081 - 0.016
cyclic di-3',5'-guanylate
additional information
cyclic di-3',5'-guanylate
0.00081
cyclic di-3',5'-guanylate
triple mutant R148A/R178A/R313A, inhibited
0.0009
cyclic di-3',5'-guanylate
wild-type
0.004
cyclic di-3',5'-guanylate
mutant R313A
0.015
cyclic di-3',5'-guanylate
double mutant R148A/R178A
0.016
cyclic di-3',5'-guanylate
triple mutant R148A/R178A/R313A
additional information
cyclic di-3',5'-guanylate
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double mutant R148A/R178A, inhibited, no activity detected
additional information
cyclic di-3',5'-guanylate
double mutant R148A/R178A, inhibited, no activity detected
additional information
cyclic di-3',5'-guanylate
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mutant R313A, inhibited, no activity detected
additional information
cyclic di-3',5'-guanylate
mutant R313A, inhibited, no activity detected
additional information
cyclic di-3',5'-guanylate
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wild-type, inhibited, no activity detected
additional information
cyclic di-3',5'-guanylate
wild-type, inhibited, no activity detected
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0.0005 - 0.033
cyclic di-3',5'-guanylate
0.0028 - 0.115
cyclic di-3',5'-guanylate
0.0005
cyclic di-3',5'-guanylate
wild-type
0.0009
cyclic di-3',5'-guanylate
mutant R313A
0.005
cyclic di-3',5'-guanylate
double mutant R148A/R178A
0.033
cyclic di-3',5'-guanylate
triple mutant R148A/R178A/R313A
0.0028
cyclic di-3',5'-guanylate
mutant R148A, 30°C, pH 8.0
0.0029
cyclic di-3',5'-guanylate
mutant R148A/R178A, 30°C, pH 8.0
0.0036
cyclic di-3',5'-guanylate
mutant R178A, 30°C, pH 8.0
0.0058
cyclic di-3',5'-guanylate
wild-type, 30°C, pH 8.0
0.1
cyclic di-3',5'-guanylate
or above, mutant R359A, 30°C, pH 8.0
0.115
cyclic di-3',5'-guanylate
mutant R390A, 30°C, pH 8.0
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malfunction
enzyme inhibition by inhibitors causes inhibition of biofilm formation of the organism
metabolism
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cyclic diguanylate (c-di-GMP) is a near universal signaling molecule produced by diguanylate cyclases that can direct a variety of bacterial behaviors. Effectors, e.g. LapD, can sense the c-di-GMP signal from a specific DGC. Relationship between DGC-effector contact and catalysis. Dynamics of a signaling complex, distinguishing interaction versus signaling, and relationship between local and global signaling, overview. Modeling
physiological function
the primary signaling molecule promoting bacterial biofilm formation is the universal second messenger cyclic di-GMP. This dinucleotide predominantly controls the gene expression of motility, adhesins, and capsule production to coordinate biofilm formation. Cyclic di-GMP is synthesized by diguanylate cyclases (DGCs) that have a GGDEF domain and is degraded by phosphodiesterases (PDEs) containing either an EAL or an HD-GYP domain
additional information
binding mode of the substrate analogue GTP-alpha-S (guanosine-alpha-thio-triphosphate) bound to PleD
additional information
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binding mode of the substrate analogue GTP-alpha-S (guanosine-alpha-thio-triphosphate) bound to PleD
additional information
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DGCs operate as dimers, using their GGDEF domains to produce c-di-GMP. In addition to GGDEF, active cyclases have also been found that make use of GGEEF, AGDEF, and GGDEM motifs
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BeF3-/Mg2+-modified PleD (100 microM) in presence of cyclic di-3,5-guanylate (0.2 mM) and substrate-analog GTPalphaS (1 mM), hanging-drop vapour-diffusion: equal volumes protein solution (10 mg/ml) and precipitant solution (0.1M HEPES pH 8, 0.73 M Na2SO4), crystals: needle shape, space group: P2(1)2(1)2(1), unit cell parameters: a: 128.9, b: 132.6, c: 88.4, resolved by molecular replacement using PDB: 1W25 as model, tightened dimer interface at the dyad symmetric stem between D1/D2 domains of the two monomers upon rotation of D2 relative to D1, restructured beta4alpha4 loop compared to nonactivated state, GTPalphaS bound to both diguanylate cyclase (GGDEF) domain active sites, 2fold symmetric crosslinking of GGDEF domains of the structural dimer in presence of cyclic di-3,5-guanylate, cyclic di-3,5-guanylate bound to allosteric (inhibitory) site similarly to nonactivated state
after activation by berillium trifluoride. Activation causes rearrangement of an adaptor domain which in turn promotes dimer formation. The substrate analogue GTPgammaS and two putative cations are bound to the active sites. Identification of a second cyclic diguanylate binding mode that crosslinks the diguanylate cyclase domains within a protein dimer and results in noncompetitive product inhibition
in complex with product cyclic diguanylate. The guanine base is H-bonded to N335 and D344, whereas the ribosyl and alpha-phosphate moieties extend over the beta2-beta3-hairpin that carries the GGEEF signature motif. In the crystal, cyclic diguanylate molecules are crosslinking active sites of adjacent dimers. In solution, two diguanylate cyclase doamins of a dimer may align in a twofold symmetric way to catalyze synthesis of cyclic diguanylate
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D327A
inactive due to loss of coordination of Mg2+
D53N
no activation by BeF3, lack of phosphoryl acceptor site
E370Q
mainly dimeric, inactive mutant of the guanylate cyclase domain GG(D/E)EF (Mg2+ coordination), no activation by BeF3 or protein concentration above 50 microM
R148A/R178A
double mutant
R148A/R178A/R313A
triple mutant, KD for binding of cyclic di-3,5-guanylate: 4 microM (10fold higher than wild-type), 60fold increased KI for product inhibition by cyclic di-3,5-guanylate, residual catalytic activity
R313A
part of inhibitory site
Y26A
dimerisation mutant, nearly inactive, mainly monomeric
D53N
less than 1% of wild-type activity
DELTAR359/DELTAD362
mutations in allosteric binding site of cyclic diguanylate, abolish cyclic diguanylate binding, strong decrease in catalytic activity
E370Q
mutation in active site, complete loss of catalytic activity without effect on allosteric binding of cyclic diguanylate
EE370GG
mutation in active site, complete loss of catalytic activity without effect on allosteric binding of cyclic diguanylate
R148A
increase in allosteric binding of cyclic diguanylate and increase in catalytic activity
R148A/R178A
increase in allosteric binding of cyclic diguanylate and increase in catalytic activity
R178A
increase in allosteric binding of cyclic diguanylate and increase in catalytic activity
R359A
mutation in allosteric binding site of cyclic diguanylate, strong decrease in cyclic diguanylate binding, strong decrease in catalytic activity
R359V
strong decrease in catalytic activity
R390A
mutation in allosteric binding site of cyclic diguanylate, strong decrease in cyclic diguanylate binding. Catalytic activity comaprable to wild-type
Y26A
almost complete loss of activity
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Paul, R.; Weiser, S.; Amiot, N.C.; Chan, C.; Schirmer, T.; Giese, B.; Jenal, U.
Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain
Genes Dev.
18
715-727
2004
Caulobacter vibrioides
brenda
Christen, B.; Christen, M.; Paul, R.; Schmid, F.; Folcher, M.; Jenoe, P.; Meuwly, M.; Jenal, U.
Allosteric control of cyclic di-GMP signaling
J. Biol. Chem.
281
32015-32024
2006
Caulobacter vibrioides (Q9A3B9)
brenda
Paul, R.; Abel, S.; Wassmann, P.; Beck, A.; Heerklotz, H.; Jenal, U.
Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization
J. Biol. Chem.
282
29170-29177
2007
Caulobacter vibrioides, Caulobacter vibrioides (Q9A5I5)
brenda
Chan, C.; Paul, R.; Samoray, D.; Amiot, N.C.; Giese, B.; Jenal, U.; Schirmer, T.
Structural basis of activity and allosteric control of diguanylate cyclase
Proc. Natl. Acad. Sci. USA
101
17084-17089
2004
Caulobacter vibrioides
brenda
Wassmann, P.; Chan, C.; Paul, R.; Beck, A.; Heerklotz, H.; Jenal, U.; Schirmer, T.
Structure of BeF3--modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition
Structure
15
915-927
2007
Caulobacter vibrioides, Caulobacter vibrioides (Q9A5I5)
brenda
Dahlstrom, K.M.; O'Toole, G.A.
A symphony of cyclases specificity in diguanylate cyclase signaling
Annu. Rev. Microbiol.
71
179-195
2017
Caulobacter vibrioides, Clostridioides difficile, Pseudomonas aeruginosa, Burkholderia cenocepacia, Vibrio cholerae serotype O1, Komagataeibacter xylinus (O87374), Escherichia coli (P0AA89), Vibrio cholerae serotype O1 A1552
brenda
Cho, K.H.; Tryon, R.G.; Kim, J.H.
Screening for diguanylate cyclase (DGC) inhibitors mitigating bacterial biofilm formation
Front. Chem.
8
264
2020
Caulobacter vibrioides (A0A0H3CCZ8), Caulobacter vibrioides (B8GZM2), Caulobacter vibrioides CB15N (A0A0H3CCZ8), Caulobacter vibrioides NA1000 (A0A0H3CCZ8), Caulobacter vibrioides NA1000 (B8GZM2), Clostridioides difficile (A0A170Y3L9), Komagataeibacter xylinus (O87374), Pseudomonas aeruginosa (Q9HT84), Pseudomonas aeruginosa (Q9HXT9), Pseudomonas aeruginosa 1C (Q9HT84), Pseudomonas aeruginosa 1C (Q9HXT9), Pseudomonas aeruginosa ATCC 15692 (Q9HT84), Pseudomonas aeruginosa ATCC 15692 (Q9HXT9), Pseudomonas aeruginosa CIP 104116 (Q9HT84), Pseudomonas aeruginosa CIP 104116 (Q9HXT9), Pseudomonas aeruginosa DSM 22644 (Q9HT84), Pseudomonas aeruginosa DSM 22644 (Q9HXT9), Pseudomonas aeruginosa JCM 14847 (Q9HT84), Pseudomonas aeruginosa JCM 14847 (Q9HXT9), Pseudomonas aeruginosa LMG 12228 (Q9HT84), Pseudomonas aeruginosa LMG 12228 (Q9HXT9), Pseudomonas aeruginosa PRS 101 (Q9HT84), Pseudomonas aeruginosa PRS 101 (Q9HXT9), Salmonella enterica subsp. enterica serovar Typhimurium (Q8ZNT5), Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 (Q8ZNT5), Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412 (Q8ZNT5), Synechocystis sp. PCC 6803 (P73272), Vibrio cholerae serotype O1 (Q9KKZ4), Vibrio cholerae serotype O1 ATCC 39315 (Q9KKZ4), Vibrio cholerae serotype O1 El Tor Inaba N16961 (Q9KKZ4)
brenda
Fernicola, S.; Paiardini, A.; Giardina, G.; Rampioni, G.; Leoni, L.; Cutruzzolxa0, F.; Rinaldo, S.
In silico discovery and in vitro validation of catechol-containing sulfonohydrazide compounds as potent inhibitors of the diguanylate cyclase PleD
J. Bacteriol.
198
147-156
2016
Caulobacter vibrioides (Q9A5I5), Caulobacter vibrioides, Caulobacter vibrioides ATCC 19089 (Q9A5I5), Caulobacter vibrioides CB15 (Q9A5I5), Pseudomonas aeruginosa (A0A0C7ADU5), Pseudomonas aeruginosa (Q9HXT9), Pseudomonas aeruginosa 1C (Q9HXT9), Pseudomonas aeruginosa ATCC 15692 (Q9HXT9), Pseudomonas aeruginosa CIP 104116 (Q9HXT9), Pseudomonas aeruginosa DSM 22644 (Q9HXT9), Pseudomonas aeruginosa JCM 14847 (Q9HXT9), Pseudomonas aeruginosa LMG 12228 (Q9HXT9), Pseudomonas aeruginosa PRS 101 (Q9HXT9)
brenda