PA4505

Summary: Correct but general; the bound nucleotide is ATP.

Reason: DppD has a Walker A ATP-binding motif in a canonical ABC ATPase domain; ATP binding (GO:0005524, a descendant) is already annotated on this gene.

Proposed replacements: ATP binding

Summary: DppD has a canonical ABC ATPase domain with a Walker A motif.

Reason: The ABC transporter domain and the Walker A ATP-binding site are clear; ATP binding is required for the ATPase that powers the Dpp importer.

Summary: DppD acts at the cytoplasmic face of the inner (plasma) membrane, bound to the DppB/DppC permeases.

Reason: As an ABC ATPase subunit DppD is peripheral rather than integral, but the plasma membrane is where it is located and active; E. coli DppD is located in the plasma membrane by IDA.

Summary: Correct but general; the supported process is dipeptide import across the plasma membrane.

Reason: The operon deletion loses dipeptide utilisation as nitrogen source and becomes phaseolotoxin resistant, both requiring uptake into the cytoplasm. Dipeptide import across plasma membrane (GO:0140206) is a descendant of peptide transport.

Proposed replacements: dipeptide import across plasma membrane

Summary: ATP hydrolysis is DppD's own catalytic activity, which powers the transport cycle.

Reason: DppD has a complete ABC ATPase domain (Walker A, ABC signature). The DppD and DppF contributions have not been separated experimentally, but both carry ABC ATPase domains. As for BraF, ATP hydrolysis activity is the subunit's own MF and the transport activity is that of the complex.

Summary: Inferred from the MF row. Correct, but DppBCDF is an importer, so the import term is more precise.

Reason: Dipeptide import across plasma membrane (GO:0140206) is an is_a descendant; the same replacement is used for DppB and DppC.

Proposed replacements: dipeptide import across plasma membrane

Summary: IBA from PTN000656114, whose IBD rests solely on PA4505's own PseudoCAP row. Correct for DppD, and the node term suits this DppD-only clade.

Reason: PA4505 in its own WITH/FROM marks its experimental seed and is expected. Unlike the DppC node PTN000766696 (which also holds NikC and GsiD), PTN000656114 contains only DppD orthologs: E. coli, Salmonella, Haemophilus and two Yersinia DppD, plus PA4505 (6 leaves in 5 taxa). E. coli DppD is the ATPase of the characterised DppABCDF dipeptide importer, so a dipeptide transporter term is a fair clade-level claim, even though the binding protein sets substrate range (E. coli Dpp also carries heme with a different binding protein, and DppD has a heme transporter IMP). Strictly the transport activity belongs to the assembled complex (contributes_to), but comparators such as E. coli DppD use enables; contributes_to is used in core_functions.

Summary: PseudoCAP row from Pletzer et al. 2014. The claim is correct, but the evidence is an operon-deletion phenotype, so the code should be IMP.

Reason: The paper deleted the whole dppBCDF operon in PA14 and found loss of dipeptide use as nitrogen source (Biolog) and resistance to phaseolotoxin. No uptake, binding or ATPase assay was done, and DppD was not mutated alone. This is a mutant phenotype, not a direct assay, but it supports the claim for DppD, whose ATPase powers the importer; phaseolotoxin resistance shows a loss of uptake specifically. Accepted, with the evidence code flagged upstream, as for DppB and DppC.

Summary: DppD is an ATPase subunit of the binding protein-dependent DppBCDF importer, whose substrate range is set by the DppA1-A5 binding proteins.

Reason: PA4505 has no complex annotation. The paper defines the dppBCDF operon and shows that a DppA1-A5 penta mutant phenocopies the operon deletion, so the system is a substrate-binding subunit-containing ABC transporter (the same term proposed for DppB and DppC). Inferred from the operon and phenotypes, hence IC.