WaaF (RfaF) is the lipopolysaccharide heptosyltransferase II of Pseudomonas aeruginosa, a 345-residue glycosyltransferase family 9 enzyme that transfers the second L-glycero-D-manno-heptose from ADP-heptose to the heptosyl-Kdo2-lipid A made by WaaC, completing the heptose backbone of the inner core oligosaccharide. The PAO1 gene restores smooth LPS to a Salmonella waaF mutant, and chromosomal null mutants could not be isolated in P. aeruginosa. waaF lies next to waaC in the PAO1 genome.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005829 cytosol | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA from PTN001575314, seeded by E. coli WaaF (P37692), which is found in cytosolic proteome fractions. Reason: WaaF is a soluble enzyme acting on a membrane-embedded lipid acceptor at the cytoplasmic face of the inner membrane; cytoplasmic in the broad sense, as for WaaC. Kept as a non-core location. Supporting Evidence: PMID:9171387 Similarly, plasmid pCOREf1 was able to complement the Salmonella waaF mutant. |
| GO:0008713 ADP-heptose-lipopolysaccharide heptosyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001575314, seeded by E. coli WaaF (P37692, IDA/EXP). GO:0008713 is defined as the heptosyltransferase II reaction, which is WaaF's activity. Reason: Correct for WaaF: TIGR02195 heptosyltransferase II family membership and complementation of the Salmonella waaF mutant. The node is too broad for this term for its WaaC and WaaQ leaves (GO_CENTRAL defect recorded on waaC), but the transfer to WaaF is right. Supporting Evidence: file:PSEAE/waaF/waaF-uniprot.txt NCBIfam; TIGR02195; heptsyl_trn_II; 1. PMID:9171387 Similarly, plasmid pCOREf1 was able to complement the Salmonella waaF mutant. |
| GO:0009244 lipopolysaccharide core region biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001575314 (seven seeds, including WaaF itself through its PseudoCAP row). Reason: WaaF catalyses a step of inner-core assembly; the IBD stands on five enterobacterial IMP seeds and the term suits a clade of LPS core heptosyltransferases. Supporting Evidence: PMID:9171387 Similarly, plasmid pCOREf1 was able to complement the Salmonella waaF mutant. |
| GO:0008713 ADP-heptose-lipopolysaccharide heptosyltransferase activity | IEA GO_REF:0000003 | ACCEPT | Summary: EC2GO mapping of EC 2.4.99.24 (heptosyltransferase II). Reason: Same claim as the accepted IBA; correct for a TIGR02195 family member. Supporting Evidence: file:PSEAE/waaF/waaF-uniprot.txt NCBIfam; TIGR02195; heptsyl_trn_II; 1. |
| GO:0009103 lipopolysaccharide biosynthetic process | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO mapping of IPR011910 (RfaF). Reason: True, but entailed by the accepted GO:0009244 lipopolysaccharide core region biosynthetic process, which is a descendant of GO:0009103. |
| GO:0009244 lipopolysaccharide core region biosynthetic process | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA electronic row for LPS core biosynthesis. Reason: Same claim as the accepted IBA and PseudoCAP rows, supported by complementation. Supporting Evidence: PMID:9171387 Similarly, plasmid pCOREf1 was able to complement the Salmonella waaF mutant. |
| GO:0016757 glycosyltransferase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO mapping of the GT9 family signatures. Reason: True, but entailed by the accepted GO:0008713 heptosyltransferase activity, which is_a glycosyltransferase activity. |
| GO:0009244 lipopolysaccharide core region biosynthetic process | IDA PMID:9171387 Isolation and characterization of two genes, waaC (rfaC) and... | ACCEPT | Summary: PseudoCAP row and a seed of the PTN001575314 IBD. The PAO1 gene complements a Salmonella waaF mutant. Reason: Heterologous complementation of a heptosyltransferase II mutant places WaaF in inner-core assembly. The evidence is genetic, so the IDA code is probably wrong; recorded as a suspected defect, as for waaC. The term is sound. Supporting Evidence: PMID:9171387 Similarly, plasmid pCOREf1 was able to complement the Salmonella waaF mutant. |
| GO:0071968 lipid A-core heptosyltransferase activity | ISS PMID:9171387 Isolation and characterization of two genes, waaC (rfaC) and... | MODIFY | Summary: PseudoCAP ISS from Salmonella WaaF (P37421). GO:0071968 names the reaction that completes lipid A-core, not the second inner-core heptose transfer. Reason: The with/from protein is heptosyltransferase II, whose reaction is exactly GO:0008713, already carried and accepted for this gene. Proposed replacements: ADP-heptose-lipopolysaccharide heptosyltransferase activity Supporting Evidence: file:PSEAE/waaF/waaF-uniprot.txt NCBIfam; TIGR02195; heptsyl_trn_II; 1. PMID:9171387 Similarly, plasmid pCOREf1 was able to complement the Salmonella waaF mutant. |
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Experiment: In vitro heptosyltransferase II assay with purified WaaF, ADP-heptose and heptosyl-Kdo2-lipid A, and conditional depletion of waaF in PAO1 with LPS core analysis by MS.
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