rmlC

Summary: Polysaccharide biosynthetic process by IBA from PTN000471580, seeded by S. enterica RfbC (P26394), M. tuberculosis RmlC (P9WH11) and this gene.

Reason: RmlC is a soluble C3/C5 epimerase that makes the nucleotide-sugar donor dTDP-L-rhamnose; it forms no glycosidic bond and adds no residue to a growing polymer, which the rhamnosyl transferases do. Supplying a donor is not participation in the polymer-forming process, so this is an over-annotation rather than a true-but-general term, and the same donor also feeds non-polymeric products elsewhere in the clade. The process RmlC does perform a step of, GO:0019305 dTDP-rhamnose biosynthetic process, is accepted in this review. The PTHR21047 family review assesses this IBD WRONG_NODE and recommends withdrawing it, and the sibling reviews of ECOLI rfbC, PSEPK rfbC and PSEPK rmlC all mark the propagated row over-annotated; an earlier version of this review called it TOO_GENERAL, which was wrong. Q9HU21 in WITH/FROM reflects its own experimental rows and is expected.

Summary: UniProt IDA from the RmlC structure and mechanism paper; one of the seeds of the PTN000471580 polysaccharide biosynthesis IBD.

Reason: Abstract only (full text not available through PMC tools). The paper shows the epimerase reaction and its mechanism, which places RmlC in dTDP-L-rhamnose synthesis, not in polymer assembly. Same judgement as the IBA row on this term: making the donor is not doing the work of polysaccharide biosynthesis.

Summary: Cytosol by IBA from E. coli RfbC (P37745).

Reason: dTDP-sugar synthesis is cytoplasmic; RmlC is a soluble cupin-fold enzyme without signal peptide or transmembrane segment.

Summary: PseudoCAP EXP, a seed of the PTN000471594 epimerase IBD. Structures of RmlC with product and product mimics, with site-directed mutants assayed for activity and deuterium exchange.

Reason: Abstract only, but UniProt's curated FUNCTION and binding-site features for this entry cite the same paper as experimental evidence (ECO:0000269), and the P. aeruginosa enzyme is among the structures solved (PDB 2IXH-2IXK). Seed verdict SOUND.

Summary: Epimerase activity by IBA from PTN000471594 (3 seeds).

Reason: Seeded by S. enterica RfbC and M. tuberculosis RmlC as well as this gene; the RmlC family (TIGR01221) is functionally uniform. Q9HU21 among the sources reflects its own experimental rows.

Summary: UniProt IDA from the same paper; another seed of PTN000471594.

Reason: Same claim and evidence as the EXP row.

Summary: EC/Rhea/InterPro mapping to the epimerase activity.

Reason: Consistent with the experimental rows.

Summary: UniProt IDA for LPS biosynthesis from the structure and mechanism paper.

Reason: The L-rhamnose whose donor RmlC makes is the core receptor for O antigen, but RmlC attaches nothing to the lipopolysaccharide: the glycosyltransferases of the core and O-antigen machinery do. The enzymology paper itself establishes the epimerase step rather than LPS synthesis. Over-annotated for the same reason as the GO:0000271 rows, and treated the same way on ECOLI rfbC (GO:0009103 ISS).

Summary: UniPathway mapping to LPS biosynthesis.

Reason: Same judgement as the IDA row on this term; the UniPathway mapping propagates the downstream assembly process to a precursor-supplying epimerase.

Summary: PseudoCAP IDA, a seed (via its GO:0000271 ancestor) of the PTN000471580 IBD. Non-polar rmlC mutants in PAO1 and PAK made a truncated core lacking the O-antigen attachment point; structural analysis of an rmd rmlC double-mutant core placed L-Rha as the receptor.

Reason: Abstract only. RmlC makes the dTDP-L-rhamnose donor for the L-Rha residue of the outer core, and rmlC mutants make a truncated core -- but that is necessity, not participation: the residue is attached by a glycosyltransferase. An earlier version of this review called precursor supply "a step of core synthesis", which is the conflation this project's rule on involved_in warns against. Marked over-annotated, consistent with the GO:0000271 and GO:0009103 rows above and with ECOLI rfbC's GO:0009243 O-antigen row. The process RmlC does perform a step of is GO:0019305, accepted here. The evidence described is mutant analysis, so IMP rather than IDA is the right code; recorded as a PROBABLE evidence-code defect.

Summary: dTDP-rhamnose biosynthetic process by IBA from PTN000471594 (2 seeds).

Reason: RmlC catalyses the third step of dTDP-L-rhamnose synthesis; seeded by M. tuberculosis RmlC and this gene's own experimental row.

Summary: PseudoCAP IDA, a seed of the PTN000471594 dTDP-rhamnose IBD.

Reason: Abstract only. The paper characterises the reaction and mechanism of the third enzyme of the rhamnose pathway, and UniProt cites it for function in dTDP-rhamnose biosynthesis. Seed verdict SOUND.

Summary: UniPathway mapping to dTDP-L-rhamnose biosynthesis.

Reason: Same claim as the experimental row.