Gene Ontology annotation through association of InterPro records with GO terms
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Global topology analysis of the Escherichia coli inner membrane proteome.
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FepE was confirmed as an inner membrane protein by large-scale PhoA/GFP topology analysis of the E. coli inner membrane proteome.
"Using C-terminal tagging with the alkaline phosphatase and green fluorescent protein, we established the periplasmic or cytoplasmic locations of the C termini for 601 inner membrane proteins."
Genetic organization of multiple fep genes encoding ferric enterobactin transport functions in Escherichia coli.
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Original identification of fepE through insertion mutagenesis. Insertions between entF and fepC disrupted iron transport via enterobactin. The gene was proposed to encode a component of the ferric enterobactin permease. However, this functional assignment has been superseded by the identification of FepE as a Wzz-family O-antigen chain length regulator.
"Another insertion mutation between entF and fepC was also shown to disrupt iron transport via enterobactin and thus defined the fepE locus; fepE weakly expressed a 43,000-dalton protein in minicells. It is proposed that these newly identified genes, fepD and fepE, provide functions which act in conjunction with the fepC product to form the ferric enterobactin-specific cytoplasmic membrane permease."
Regulation of Salmonella typhimurium lipopolysaccharide O antigen chain length is required for virulence; identification of FepE as a second Wzz.
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Demonstrated that FepE (WzzfepE) is a second Wzz protein in Salmonella typhimurium responsible for very long modal length O-antigen (>100 repeat units). Established that bimodal O-antigen chain length distribution is important for complement resistance and virulence.
"In addition to the previously described wzzST that results in long (L) modal length LPS with 16-35 Oag repeat units (RUs), we now report that wzzfepE, a homologue of Escherichia coli fepE, is responsible for the production of very long (VL) modal length LPS Oag, estimated to contain> 100 Oag RUs"
Structural characterization of closely related O-antigen lipopolysaccharide (LPS) chain length regulators.
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Determined crystal structure of FepE mutant. Showed FepE is a polysaccharide co-polymerase (PCP-1 family) whose structure determines O-antigen modal chain length. Mutations in FepE severely attenuate very long O-antigen polymer production.
"We also present the structure of a Wzz FepE mutant, which exhibits severe attenuation in its ability to produce very long O-antigen polymers."
Site-directed mutagenesis reveals key residue for O antigen chain length regulation and protein stability in Pseudomonas aeruginosa Wzz2.
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Used the solved E. coli Wzz FepE crystal structure as a reference for mapping residues important for chain length regulation. Confirmed that Wzz proteins form oligomeric assemblies essential for chain length regulating activity.
"Mapping residue 321 onto the solved Escherichia coli Wzz FepE crystal structure predicted it to be located within alpha helix 8, which participates in intermonomeric interactions."
Residues located inside the Escherichia coli FepE protein oligomer are essential for lipopolysaccharide O-antigen modal chain length regulation.
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Detailed mutagenesis study of E. coli K-12 FepE demonstrating it confers very-long (VL) O-antigen modal chain length of >80 repeat units. Critical residues L168 and D268 inside the oligomer cavity are essential for chain length regulation. FepE is explicitly treated as a PCP1a/Wzz-family O-antigen chain length regulator, not a ferric enterobactin transporter.
"FepE regulates LPS O-antigen modal chain length and confers a very-long O-antigen phenotype of more than 80 repeat units"
Repeat-Unit Elongations To Produce Bacterial Complex Long Polysaccharide Chains, an O-Antigen Perspective
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Mechanistic review establishing that Wzz proteins regulate Wzy polymerase processivity. Free Wzy produces short non-modal chains (1-3 units), while Wzz-associated Wzy produces longer modal distributions. This framing applies to FepE as a Wzz family member.
"Free Wzy tends to produce short non-modal chains, whereas Wzy coupled to Wzz can yield longer modal distributions"
The lipid linked oligosaccharide polymerase Wzy and its regulating co-polymerase, Wzz, from enterobacterial common antigen biosynthesis form a complex
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Cryo-EM evidence for direct Wzz-Wzy complex formation with approximately 8 Wzz to 1 Wzy stoichiometry, supporting a scaffold/regulator model for chain length control applicable to FepE and other Wzz family members.
"Wzz and Wzy form a complex with approximately 8 Wzz to 1 Wzy stoichiometry in vivo"
Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.
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Identified FepE as an example of a frequency-biased AI prediction error. DeepECTF incorrectly predicted histidine kinase activity (EC 2.7.13.3) for FepE, which has no sequence similarity to kinase families.
"out of the 12 proteins annotated as histidine kinase (EC 2.7.13.3) in the 453 DeepECTF predictions, none of them have sequence similarity to histidine kinase families, and 8 have been annotated with different and experimentally validated functions (such as ferric enterobactin transport protein FepE for b0587)"
GOA annotations for E. coli fepE
OpenScientist hypothesis report for fepE protein tyrosine kinase activity
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OpenScientist refuted the fepE protein tyrosine kinase activity hypothesis and identified the IBA as a PANTHER family over-annotation.
"FepE possesses **only** that periplasmic Wzz domain and does **not** carry the cytoplasmic BY-kinase machinery."