PA3047 (Q9HZG1) notes

Penicillin-binding protein 4 (PBP4, dacB), peptidase S13 family, predicted signal peptide
(SignalP 1-22). No deep-research provider was available; literature search by hand (full text
of PMID:25495032 in the cache, PMC4304477; QuickGO for the E. coli DacB and Dictyostelium pscA
seeds).

Literature

Lee et al. 2015 (PMID:25495032; full text): purified PBP4 (residues 23-476) is a bifunctional
DD-carboxypeptidase/4,3-endopeptidase ["PBP4 is a bifunctional enzyme having both
dd-carboxypeptidase and endopeptidase activities."; "The endopeptidase activity is specific to
hydrolysis of 4,3-cross-linked peptidoglycan."; "PBP4 catalyzes both reactions equally well."].
The DD-carboxypeptidase assay used synthetic pentapeptides ending D-Ala-D-Ala. Cefoxitin
induction raises pentapeptide and 4,3-cross-linked material that enters muropeptide recycling.
No biosynthetic step is measured.
E. coli DacB (P24228): IMP GO:0000270 (PMID:2046551), IMP GO:0009002 (PMID:331322), ISM
GO:0004185. Dictyostelium pscA (Q86I79): dictyBase IDA GO:0004185 (PMID:12843630).

Review decisions

GO:0000270 IBA: ACCEPT. GO:0004175 IDA: ACCEPT.
GO:0004185 (IBA, IEA, IDA): MODIFY to GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase.
GO:0006508 proteolysis IEA: MARK_AS_OVER_ANNOTATED (substrate is peptidoglycan, not protein).
GO:0009252 IDA: MODIFY to GO:0000270; PSEUDOCAP WRONG_TERM defect, PROBABLE.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN000768632	GO:0000270 peptidoglycan metabolic process	2	20 (18 taxa)	GO:0009252 peptidoglycan biosynthetic process, IDA, PMID:25495032 (PseudoCAP)	OVER-SPECIFIC	Full text: only hydrolytic activities (DD-CPase, 4,3-endopeptidase) are shown, tied to muropeptide recycling; biosynthesis is not shown. PAINT already placed the parent GO:0000270, which the paper supports. PSEUDOCAP WRONG_TERM defect, PROBABLE.	E. coli DacB P24228 (IMP GO:0000270, PMID:2046551)	Yes, on DacB
PTN000768632	GO:0004185 serine-type carboxypeptidase activity	3	20 (18 taxa)	GO:0004185, IDA, PMID:25495032 (PseudoCAP)	SOUND	Full text: purified PBP4 trims the terminal D-Ala of stem pentapeptides; the specific term would be GO:0009002, but the node term is right for the clade.	E. coli DacB P24228 (ISM; IMP GO:0009002); Dictyostelium pscA Q86I79 (IDA GO:0004185, PMID:12843630)	Yes, on pscA IDA (and DacB)

No GO_CENTRAL defect. Open point: GO:0000270 propagates to Dictyostelium pscA, which has no cell
wall peptidoglycan; recorded as a suggested question rather than a defect, because pscA may act
on ingested bacterial peptidoglycan.

Session 2026-11-12: consolidated with the retired dacB review; two decisions changed

This folder duplicated genes/PSEAE/dacB, which main had added for the same accession (Q9HZG1)
through the peptidoglycan-module pass. PA3047 survives as the folder name, because GOA/PseudoCAP
give the symbol as PA3047 and UniProt records no GN Name for the accession, only
OrderedLocusNames=PA3047. The dacB pass was right on both rows where the two disagreed, so the
Review decisions above are superseded on those two points:

GO:0004175 endopeptidase activity IDA: was ACCEPT, on the stated ground that GO has no term for
the 4,3 DD-endopeptidase reaction on peptidoglycan. That premise was false. GO:0061785
peptidoglycan endopeptidase activity exists ("An endopeptidase activity that uses peptidoglycan as
a substrate"), is in cache/go/terms.csv, and OLS lists GO:0004175 among its ancestors (checked
2026-11-12). Now MODIFY to GO:0061785, and the second core function declares it.
GO:0006508 proteolysis IEA: was MARK_AS_OVER_ANNOTATED. Now REMOVE, with an INTERPRO
DELETE_VALUE defect on the IPR000667 (Peptidase S13) to GO:0006508 mapping. PBP4 acts on the stem
peptides and cross-links of the sacculus, not on proteins, so the claim is wrong rather than
merely broad — the sanctioned use of REMOVE on a demonstrably wrong electronic mapping, with the
upstream fix recorded as well as the local one.

Also carried across from the dacB pass: a NEW IC row for GO:0030288 outer membrane-bounded
periplasmic space (SignalP signal peptide 1-22 in the UniProt record, plus the periplasmic location
of the peptidoglycan substrate), locations on both core functions, and PMID:27716106 with its
in vivo finding that the D,D-endopeptidase activity predominates.