Gene Ontology annotation through association of InterPro records with GO terms
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
Functional Role of Lanthanides in Enzymatic Activity and Transcriptional Regulation of Pyrroloquinoline Quinone-Dependent Alcohol Dehydrogenases in Pseudomonas putida KT2440.
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Purified target proteins oxidize both primary and secondary alcohols; artificial acceptor assays do not establish their native cytochrome partner.
"Similarly, 2-phenylethanol, the secondary alcohol 2-butanol, cinnamyl alcohol, and the acyclic sesquiterpene farnesol were efficiently converted, with specific activities ranging from 6.7 ± 1.1 to 2.0 ± 0.3 U mg−1."
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Target proteins were purified recombinantly from E. coli; that host is not the native organism.
"A one-step affinity chromatography method produced soluble C-terminally His-tagged PedE and PedH to visible purity (see Fig. S1 in the supplemental material) from cell lysates of Escherichia coli BL21(DE3)."
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Calcium-dependent PedE contrasts with lanthanide-dependent PedH.
"While PedE showed enzyme activity at concentrations of 10 µM to 10 mM CaCl2, with a peak in activity at 1 mM"
The PedS2/PedR2 Two-Component System Is Crucial for the Rare Earth Element Switch in Pseudomonas putida KT2440.
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Both proteins are type I quinoproteins in a native periplasmic oxidation system.
"For efficient capture and metabolism of such VOCs, P. putida makes use of two pyrroloquinoline quinone (PQQ)-dependent ethanol dehydrogenases (PQQ-EDHs)—namely, PedE and PedH—to carry out the initial oxidation steps in the periplasm of the cell (7, 8)."
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PedS2/PedR2 controls expression; PedH-dependent feedback has an unresolved mechanism.
"In addition, the transcription of pedH is activated via a yet unknown pathway, in which a functional PedH protein is an essential component, most likely by acting as a lanthanide sensor (8)."
Dehydrogenation Mechanism of Three Stereoisomers of Butane-2,3-Diol in Pseudomonas putida KT2440.
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Native deletion and lanthanum rescue distinguish condition-dependent (2S,3S)-butanediol entry; this is not a purified stereospecificity assay.
"Double-knockout strain P. putida KT2440 (ΔpedEΔpedH) was completely unable to utilize (2S,3S)-2,3-BDO both in the presence and absence of La3+ (Figures 5C,D)"
pedE curated UniProt record
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The cytochrome c550 acceptor assignment is explicitly by similarity, not native partner identification.
"Uses a specific inducible cytochrome c550,
CC encoded by the adjacent gene in the locus, as electron acceptor (By
CC similarity)."