PA1486 (Q9I3M6) notes

Identity

PA1486 is bapF, the beta-peptidyl aminopeptidase BapF of P. aeruginosa PAO1. The Pseudomonas Genome
Database lists PA1486 as bapF ("beta-peptidyl aminopeptidase"), and MEROPS files BapF as P01.003,
matching the DR MEROPS; P01.003 line on Q9I3M6.
Family: peptidase S58/DmpA (Pfam PF03576 Peptidase_S58; InterPro IPR005321 Peptidase_S58_DmpA; CDD
cd02253 DmpA; PANTHER PTHR36512 D-AMINOPEPTIDASE). These are N-terminal-nucleophile (Ntn) hydrolases that
autoprocess at a Gly-Ser bond and use the new N-terminal serine as nucleophile.
Own sequence check (UniProt sequence, positions 230-245: EGTPGMGSIVVILATD): residue 237 is Ser,
preceded by Gly236, i.e. the canonical DmpA-family Gly-Ser autoprocessing site. This matches the
"catalytic Ser" S237 mutated in PMID:23728237.

PMID:23728237
PMID:23728237 — direct in vitro aminopeptidase (N-terminal beta-amino acid
release) activity of the purified recombinant enzyme.
PMID:23728237 — aminolysis (transpeptidation) in addition to hydrolysis.
The cached paper is abstract-only. Earlier BapF work from the Arima group (2010-2011, Appl Environ
Microbiol / FEBS J) is not in the cache; I did not find it via the PubMed MCP search.
No physiological substrate or phenotype is known for PA1486.

No GO term exists for beta-peptidyl aminopeptidase (EC 3.4.11.25); searched OLS and the local GO db.
GO:0070009 serine-type aminopeptidase activity (child of GO:0004177) fits the catalytic-Ser Ntn
mechanism shown by the S237 mutagenesis.

GO:0004177 aminopeptidase activity, IDA PseudoCAP (PMID:23728237): MODIFY to GO:0070009 serine-type
aminopeptidase activity (the paper itself identifies Ser237 as the catalytic residue). The aminopeptidase
claim is sound.
GO:0004177 aminopeptidase activity, IBA (PTN002194605): MODIFY to GO:0070009 (consistent with the IDA row; the node term itself is sound for the clade). The seed is direct biochemistry and
aminopeptidase activity is the characterised activity of the DmpA family (D-aminopeptidase DmpA,
beta-peptidyl aminopeptidases BapA/BapF).

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002194605	GO:0004177 aminopeptidase activity	1 (sole)	12 (12 taxa)	GO:0004177, IDA, PMID:23728237 (PseudoCAP)	SOUND	Purified recombinant BapF (PA1486) releases p-nitroaniline from beta-homoGly-pNA, a direct aminopeptidase assay. The generic aminopeptidase term (not a beta-peptide-specific one) is appropriately broad for a 12-leaf S58/DmpA subclade whose members include D-aminopeptidases and beta-peptidyl aminopeptidases with differing stereo-specificity.