wbpD

Summary: PseudoCAP IDA polysaccharide biosynthetic process from the in vitro reconstitution of the UDP-ManNAc3NAcA nucleotide-sugar pathway.

Reason: True but general. WbpD makes a nucleotide-sugar precursor of the B-band O-antigen repeat, so the polysaccharide it contributes to is the O antigen. GO:0009243 O antigen biosynthetic process is an is_a descendant of polysaccharide biosynthetic process and is already carried by this gene (IDA, EXP, IEA), so the row should be refined to it.

Proposed replacements: O antigen biosynthetic process

Summary: PseudoCAP EXP UDP-glucuronate biosynthetic process; sole seed of the PAINT IBD at PTN001292385.

Reason: The process is wrong as stated. GO:0006065 is the formation of UDP-glucuronate (UDP-GlcA). WbpD acetylates UDP-GlcNAc3NA to UDP-GlcNAc3NAcA in the synthesis of UDP-ManNAc3NAcA from UDP-GlcNAc; UDP-glucuronate is neither a substrate nor a product of the Wbp pathway (even the first step, WbpA, oxidises UDP-GlcNAc, not UDP-Glc). The products are glucuronic-acid derivatives, which probably explains the choice. In addition, PMID:16102001 states that no substrate was available, so it could not demonstrate any nucleotide-sugar biosynthesis directly; the knockout phenotype it reports is loss of B-band O antigen. The sound essence is nucleotide-sugar biosynthesis (shown by PMID:19282284 and PMID:19348502), so the row is modified to the parent GO:0009226 nucleotide-sugar biosynthetic process; no GO term exists for UDP-ManNAc3NAcA biosynthesis.

Proposed replacements: nucleotide-sugar biosynthetic process

Summary: IBA UDP-glucuronate biosynthetic process from PTN001292385, whose sole seed is the PseudoCAP EXP row on WbpD itself.

Reason: Same claim as the EXP row and wrong for the same reason; WbpD's own appearance in WITH/FROM is expected (it is the seed), but the seed term is a mis-chosen process. The nucleotide-sugar biosynthesis essence is correct for WbpD and very probably for the small WbpD/WlbB-like clade under the node (B. pertussis WlbB is a functional homolog), so the row is modified to GO:0009226 nucleotide-sugar biosynthetic process, and the node is reported to GO Central.

Proposed replacements: nucleotide-sugar biosynthetic process

Summary: O antigen biosynthetic process from the wbpD knockout and complementation.

Reason: The knockout lacks long-chain B-band O antigen and semi-rough LPS and is complemented in trans; WbpD itself catalyses a step (nucleotide-sugar precursor formation) of the pathway, so this is participation, not only necessity. Core process.

Summary: Same claim as the EXP row from the same paper.

Reason: Consistent with the EXP row; the evidence in the abstract is genetic (knockout and complementation), but the claim is correct and supported by later biochemistry.

Summary: O antigen biosynthetic process from the in vitro characterization of WbpB, WbpE and WbpD.

Reason: WbpD catalyses the 3-N-acetylation step in formation of the UDP-ManNAc3NAcA donor of the B-band O antigen; the five enzymes reconstitute the donor in vitro.

Summary: UniPathway mapping (LPS O-antigen biosynthesis).

Reason: Consistent with the experimental rows.

Summary: PseudoCAP EXP acetyltransferase activity; sole seed of the PAINT IBD at PTN001917401.

Reason: Correct and directly supported: the WbpD product UDP-GlcNAc3NAcA was detected by MALDI-TOF MS in coupled reactions and its structure solved by NMR (PMID:19282284), with kinetics in PMID:19348502. The acetyl group is transferred to the C3 amino nitrogen, so the more specific existing term is GO:0008080 N-acetyltransferase activity (is_a acetyltransferase activity); GO has no term for EC 2.3.1.201 itself. The seed is sound.

Proposed replacements: N-acetyltransferase activity

Summary: IBA acetyltransferase activity from PTN001917401, seeded only by the WbpD EXP row.

Reason: The IBD is sound; WbpD in its own WITH/FROM reflects the experimental seed and is not circular. Acetyltransferase activity is an appropriately broad term for the node (67 leaves, 28 taxa of hexapeptide-repeat acetyltransferases), but for WbpD itself the activity is known to be an N-acetyltransferase, so for consistency with the EXP row this gene's annotation is refined to GO:0008080. No change is requested at the node.

Proposed replacements: N-acetyltransferase activity

Summary: UniProt IDA acyltransferase activity from the WbpD kinetic study.

Reason: Correct but general; the transferred acyl group is acetyl and the acceptor is an amino nitrogen, so GO:0008080 N-acetyltransferase activity (a descendant) is supported.

Proposed replacements: N-acetyltransferase activity

Summary: Protein trimerization from SDS-PAGE, MALDI-TOF and gel filtration of His6-WbpD.

Reason: WbpD is a homotrimer, as expected for hexapeptide acyltransferases whose active sites lie between subunits. Self-assembly into the trimer is real but is a structural property of the enzyme, not its biological role.