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Literature summary for 3.1.4.52 extracted from

  • Chao, L.; Rakshe, S.; Leff, M.; Spormann, A.M.
    PdeB, a cyclic Di-GMP-specific phosphodiesterase that regulates Shewanella oneidensis MR-1 motility and biofilm formation (2013), J. Bacteriol., 195, 3827-3833.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.1.4.52

Cloned(Commentary)

Cloned (Comment) Organism
gene pdeB, gene expression profiling and quantitative PCR in wild-type and mutant cells, expression of GFP-tagged mutant enzymes, expression of N-terminally maltose-binding protein tagged and C-terminally His6 tagged truncated wild-type enzyme and mutant E364A in Escherichia coli strain Tuner(DE3)pLysS Shewanella oneidensis

Protein Variants

Protein Variants Comment Organism
E634A site-directed mutagenesis Shewanella oneidensis
additional information generation of GFP-tagged or untagged markerless in-frame deletion mutants and chromosomal gene replacement Shewanella oneidensis

Localization

Localization Comment Organism GeneOntology No. Textmining
membrane the transmembrane protein contains two transmembrane segments, positions 7 to 29 and 230 to 252 Shewanella oneidensis 16020
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Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
cyclic di-3',5'-guanylate + H2O Shewanella oneidensis
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 5'-phosphoguanylyl(3'->5')guanosine
-
 ?
cyclic di-3',5'-guanylate + H2O Shewanella oneidensis MR-1 / ATCC 700550
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 5'-phosphoguanylyl(3'->5')guanosine
-
 ?

Organism

Organism UniProt Comment Textmining
Shewanella oneidensis Q8EJM6 PNNL strain, gene pdeB
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Shewanella oneidensis MR-1 / ATCC 700550 Q8EJM6 PNNL strain, gene pdeB
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Purification (Commentary)

Purification (Comment) Organism
recombinant N-terminally maltose-binding protein tagged and C-terminally His6 tagged truncated wild-type enzyme and mutant E364A from Escherichia coli strain Tuner(DE3)pLysS by nicel affinity and amylose affinity chromatography Shewanella oneidensis

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
cyclic di-3',5'-guanylate + H2O
-
 Shewanella oneidensis 5'-phosphoguanylyl(3'->5')guanosine
-
 ?
cyclic di-3',5'-guanylate + H2O
-
 Shewanella oneidensis MR-1 / ATCC 700550 5'-phosphoguanylyl(3'->5')guanosine
-
 ?

Subunits

Subunits Comment Organism
More enzyme domain structure analysis, overview Shewanella oneidensis

Synonyms

Synonyms Comment Organism
c-di-GMP-hydrolyzing-phosphodiesterase
-
 Shewanella oneidensis
PAS-GGDEF-EAL domain-containing protein
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 Shewanella oneidensis
PDE
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 Shewanella oneidensis
PdeB
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 Shewanella oneidensis
SO0437
-
 Shewanella oneidensis

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
30
-
 assay at Shewanella oneidensis

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.6
-
 assay at Shewanella oneidensis

General Information

General Information Comment Organism
malfunction a pdeB deletion mutant exhibits decreased swimming motility and increased biofilm formation under rich growth medium conditions, which is consistent with an increase in intracellular c-di-GMP. A mutation inactivating the EAL domain also produces similar swimming and biofilm phenotypes, indicating that the increase in c-di-GMP is likely due to a loss in phosphodiesterase activity. Transcriptional profiling by DNA microarray analysis of biofilms of pdeB (in-frame deletion and EAL) mutant cells reveals that expression of genes involved in sulfate uptake and assimilation are repressed. Addition of sulfate recovers cell mobility of the mutants Shewanella oneidensis
physiological function the organism forms biofilms on mineral surfaces through a process controlled by the cyclic dinucleotide messenger c-di-GMP. Cellular concentrations of c-di-GMP are maintained by proteins containing GGDEF and EAL domains, which encode diguanylate cyclases for c-di-GMP synthesis and phosphodiesterases for c-di-GMP hydrolysis, respectively. The enzyme PdeB contains a GGDEF-EAL multidomain and an additional Per-Arnt-Sim (PAS) sensor domain. The purified enzyme PdeB exhibits phosphodiesterase activity via the EAL domain, but no diguanylate cyclase activity Shewanella oneidensis