PA3047 (dacB) encodes penicillin-binding protein 4 (PBP4) of Pseudomonas aeruginosa, a low-molecular-mass PBP of the peptidase S13 family with a predicted N-terminal signal peptide. Purified PBP4 is a bifunctional peptidoglycan hydrolase. As a DD-carboxypeptidase it removes the terminal D-Ala from the stem pentapeptide, and as a DD-endopeptidase it cleaves 4,3 (D-Ala-mDAP) cross-links but not 3,3 cross-links, with similar efficiency for both reactions. PBP4 is a target of beta-lactams such as cefoxitin. Loss of PBP4 function, by mutation in clinical isolates or by beta-lactam inhibition, leads to high-level expression of the AmpC beta-lactamase, probably because muropeptides it would otherwise process enter the recycling pathway that signals through AmpR.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000270 peptidoglycan metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000768632 (peptidase S13 / PBP4 clade; 2 seeds for this term, 20 leaf IBAs). Seeds are E. coli DacB (P24228, IMP acts_upstream_of_or_within, PMID:2046551) and PA3047 (PseudoCAP IDA for the child term GO:0009252, PMID:25495032). Reason: PBP4 hydrolyses the stem peptides and 4,3 cross-links of peptidoglycan, so it acts in peptidoglycan metabolism; this is the level the evidence supports (see the GO:0009252 row). The IBD stands on the E. coli DacB seed. Supporting Evidence: PMID:25495032 The endopeptidase activity is specific to hydrolysis of 4,3-cross-linked peptidoglycan. |
| GO:0004185 serine-type carboxypeptidase activity | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN000768632 (3 seeds). Seeds are PA3047 (PseudoCAP IDA), E. coli DacB (P24228, ISM for this term and IMP for the child GO:0009002) and Dictyostelium pscA (Q86I79, dictyBase IDA, PMID:12843630). Reason: Correct but general for PA3047. The carboxypeptidase activity shown is removal of the terminal D-Ala from the D-Ala-D-Ala stem pentapeptide, which is GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity (is_a GO:0004185). The node term itself is sound and suitably broad for the clade; the IBD stands on the Dictyostelium IDA seed without PA3047. Propagation Review Root cause: NO FAILURE CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000768632 Β· PTN000768632 SUPPORTS TRANSFER Peptidase S13 clade spanning bacteria and Dictyostelium; the generic serine-type carboxypeptidase term suits it. UniProtKB:Q9HZG1 Β· PA3047 (self; PseudoCAP IDA, PMID:25495032) SUPPORTS TRANSFER Expected self-seed reflecting the target's own purified-enzyme evidence. UniProtKB:P24228 Β· E. coli DacB SUPPORTS TRANSFER ISM for GO:0004185; IMP for GO:0009002 (PMID:331322). dictyBase:DDB_G0271902 Β· Dictyostelium pscA (Q86I79) SUPPORTS TRANSFER dictyBase IDA for GO:0004185 (PMID:12843630). Proposed replacements: serine-type D-Ala-D-Ala carboxypeptidase activity Supporting Evidence: PMID:25495032 the two synthetic pentapeptide substrates (18 and 19) were evaluated for the hydrolytic removal of the terminal d-Ala to give tetrapeptide products |
| GO:0004185 serine-type carboxypeptidase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO from the peptidase S13 signature. Reason: Correct but general; the assayed activity is D-Ala-D-Ala carboxypeptidase (GO:0009002). Proposed replacements: serine-type D-Ala-D-Ala carboxypeptidase activity Supporting Evidence: file:PSEAE/PA3047/PA3047-uniprot.txt Pfam; PF02113; Peptidase_S13 PMID:25495032 the two synthetic pentapeptide substrates (18 and 19) were evaluated for the hydrolytic removal of the terminal d-Ala to give tetrapeptide products |
| GO:0006508 proteolysis | IEA GO_REF:0000002 | REMOVE | Summary: InterPro2GO proteolysis from the peptidase S13 signature. Reason: GO:0006508 is defined as "The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds." PBP4 acts on the stem peptides and cross-links of the peptidoglycan sacculus, not on proteins, so the claim is wrong rather than merely broad, and the process it does take part in is peptidoglycan metabolism (GO:0000270, asserted elsewhere in this review). This is the sanctioned use of REMOVE on a demonstrably wrong electronic mapping, with the upstream fix recorded rather than only the local one. Treated the same way in the sibling PBP4/PBP7 reviews of the AST-adjacent peptidoglycan module. Supporting Evidence: PMID:25495032 PBP4 is a bifunctional enzyme having both dd-carboxypeptidase and endopeptidase activities. PMID:25495032 These data demonstrate that PBP4 has dual dd-carboxypeptidase and 4,3-endopeptidase activities with respect to the stem peptide of the sacculus. |
| GO:0004175 endopeptidase activity | IDA PMID:25495032 Catalytic spectrum of the penicillin-binding protein 4 of Ps... | MODIFY | Summary: PseudoCAP IDA. Purified PBP4 hydrolysed a synthetic 4,3-cross-linked muropeptide but not 3,3 cross-links. Reason: Full text read; direct enzymology on purified PBP4. Correct but general: the assayed substrate is peptidoglycan, and GO:0061785 peptidoglycan endopeptidase activity ("An endopeptidase activity that uses peptidoglycan as a substrate") is a descendant of GO:0004175 (is_a checked in OLS, 2026-11-12). An earlier version of this review claimed no such term existed; that was wrong. GO still has no term for the 4,3 versus 3,3 cross-link specificity shown here, and the serine-type parent implied by the S13 family was not assayed, so GO:0061785 is as specific as the evidence supports. Proposed replacements: peptidoglycan endopeptidase activity Supporting Evidence: PMID:25495032 The endopeptidase activity is specific to hydrolysis of 4,3-cross-linked peptidoglycan. |
| GO:0004185 serine-type carboxypeptidase activity | IDA PMID:25495032 Catalytic spectrum of the penicillin-binding protein 4 of Ps... | MODIFY | Summary: PseudoCAP IDA. Purified PBP4 removed the terminal D-Ala from synthetic stem pentapeptides (kcat/Km about 10^4 M-1 s-1). Reason: Full text read. The activity is right and directly shown, so the seed is SOUND for PTN000768632; the specific term for the reaction assayed is GO:0009002 serine-type D-Ala-D-Ala carboxypeptidase activity (is_a GO:0004185). Proposed replacements: serine-type D-Ala-D-Ala carboxypeptidase activity Supporting Evidence: PMID:25495032 the two synthetic pentapeptide substrates (18 and 19) were evaluated for the hydrolytic removal of the terminal d-Ala to give tetrapeptide products |
| GO:0009252 peptidoglycan biosynthetic process | IDA PMID:25495032 Catalytic spectrum of the penicillin-binding protein 4 of Ps... | MODIFY | Summary: PseudoCAP IDA for peptidoglycan biosynthesis, citing the in vitro characterisation of PBP4 hydrolase activities. Reason: Full text read. The paper shows only hydrolytic reactions (DD-carboxypeptidase trimming and 4,3 cross-link cleavage) and links them to muropeptide release and recycling; it reports no synthetic step and no in vivo role in building the sacculus. PBP4 acts in peptidoglycan metabolism, the level PAINT placed on PTN000768632, but biosynthesis is not shown. This seed row is OVER-SPECIFIC. Proposed replacements: peptidoglycan metabolic process Supporting Evidence: PMID:25495032 In the presence of Ξ²-lactam antibiotics these altered cell-wall segments enter into the muropeptide recycling pathway |
| GO:0030288 outer membrane-bounded periplasmic space | IC PMID:25495032 Catalytic spectrum of the penicillin-binding protein 4 of Ps... | NEW | Summary: A predicted N-terminal signal peptide exports PBP4 to the periplasm, where its peptidoglycan substrate lies. Reason: Two independent lines agree, which is the bar this project sets for adding a sub-compartment: SignalP predicts a cleavable signal peptide (residues 1-22), and the enzyme hydrolyses the peptidoglycan sacculus, which in a diderm bacterium lies in the outer membrane-bounded periplasm. The authors of the enzymology paper describe the same N-terminal segment as the periplasmic delivery signal. GO:0030288 is the term used for the PBP4 orthologs in the sibling reviews. Supporting Evidence: file:PSEAE/PA3047/PA3047-uniprot.txt SIGNAL 1..22 PMID:25495032 This construct lacks the signal peptide for delivery to the periplasm but possesses the membrane-anchor segment. |
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Download this section (compressed HTML)Q: PTN000768632 propagates GO:0000270 peptidoglycan metabolic process to Dictyostelium pscA, an organism without a peptidoglycan wall. Does pscA act on ingested bacterial peptidoglycan, or should the process IBD be restricted to the bacterial subclade?
Q: Which PBP4 product or unprocessed substrate (pentapeptide or 4,3-cross-linked muropeptide) is the signal that derepresses AmpC when PBP4 is inactivated?
Experiment: Compare periplasmic and cytoplasmic muropeptide pools of PAO1, a dacB (PA3047) deletion and a catalytic-serine mutant by LC-MS, together with ampC expression, to identify the signalling muropeptide.
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