lasB (PA3724, P14756) — curation notes

Gene identity

UniProt P14756, ELAS_PSEAE, 498 aa precursor, reviewed; PseudoCAP PA3724;
matches the worklist accession. EC 3.4.24.26; MEROPS M04.005; peptidase M4
(thermolysin) family; PANTHER PTHR33794:SF1 ("bacillolysin"). 19 PDB entries,
most of the mature chain 198-498 (1EZM at 1.5 A), three of 24-498.

Chain structure (UniProt FT): SIGNAL 1-23, PROPEP 24-197, mature elastase
198-498; SITE 197..198 "Cleavage; by autolysis"; ACT_SITE 338 and 420 (proton
donor); catalytic Zn(2+) at His337/His341/Glu361; Ca(2+) at
Asp333/Asp369/Glu372/Asp380/Asp382; disulfides 227-255 and 467-494.
Literature residue numbers are usually on the mature chain (His-223 = His420).

What is established

Zinc metalloprotease with the thermolysin fold PMID:1899664,
28% identity to thermolysin, "the active site cleft is significantly more
'open' in PAE than in thermolysin". UniProt: 1 Zn(2+) and 1 Ca(2+) per
subunit; monomer; inhibited by phosphoramidon.
Catalysis and autoprocessing. Active-site His substitutions abolish activity
PMID:1744034 and block
maturation, while mature elastase processes the mutant pro-enzymes in trans;
"The present results confirm that His-223 is essential for elastase activity
and provide evidence for autoproteolytic processing of proelastase."
Substrates. UniProt CC:FUNCTION: "Cleaves host elastin, collagen, IgG, and
several complement components as well as endogenous pro-aminopeptidase";
CC:CATALYTIC ACTIVITY: "Hydrolysis of proteins including elastin, collagen
types III and IV, fibronectin and immunoglobulin A, generally with bulky
hydrophobic group at P1'." Maturation of pro-PaAP depends on LasB
PMID:11533066; LasB also
processes pro-CbpD [PMID:9642203 per UniProt].
Export and location. Secreted; "We demonstrate that the propeptide and the
mature elastase are both secreted but that the propeptide is degraded
extracellularly." PMID:9642203; "The signal sequence is cleaved off during
transport across the inner membrane and, in the periplasm, proelastase is
further processed." UniProt: "Secreted in an Xcp-dependent fashion (a type II
secretion pathway)."
Metal requirement for production. PMID:1597429
Virulence. Deletion in an early-persistence CF isolate reduces burden in a
murine persistent-pneumonia model; "The zinc metalloprotease elastase B (also
called LasB or pseudolysin) is the most abundant protease in the P."
PMID:33510733.
Surface behaviour. "Elastase LasB and PvdQ are essential for normal swarming
behavior." and "all four tested lasB mutants also showed a strong impairment
in biofilm formation with about 50% less biomass"; both complemented
PMID:18245294. The authors link this to T2SS secretion rather than to a
motility or matrix role of LasB itself.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale
PTN002138658	GO:0006508 proteolysis	1 (sole seed)	21 (10 taxa, PAINT leaf GAF)	GO:0006508, IDA, PMID:1597429 (PseudoCAP)	SOUND	The seed records the gene's own activity, not a downstream phenotype: supernatant proteolytic and elastolytic activity tracking with the mature 33 kDa elastase, with zinc-dependent recovery of activity in the assay. The claim is independently certain for LasB (EC 3.4.24.26, thermolysin-like active site resolved at 1.5 A, His-223 mutants inactive). The reference is a weaker choice than PMID:1899664/PMID:1744034 but is not wrong, so no PseudoCAP defect is raised. The node term is maximally conservative for a clade of 21 M4 thermolysin-family metalloproteinases (Bacillus bacillolysins, Listeria Mpl, Vibrio HA/protease, Leptospira thermolysins, Streptomyces neutral metalloproteinases), and the substrate specificity and virulence context were not propagated.

PseudoCAP's other rows for PA3724 (GO:0015628, GO:0043952, GO:0044010,
GO:0071978) seed no IBD, but two of them are over-annotations:

GO:0015628 protein secretion by the type II secretion system (IDA,
PMID:9642203) and GO:0043952 protein transport by the Sec complex (IDA, same
paper) treat the cargo as a participant in its own export. Flagged as
PROBABLE PseudoCAP WRONG_TERM/CHECK defects, exactly as previously recorded
for PaAP (genes/PSEAE/lap) from the same reference.
GO:0044010 and GO:0071978 (IMP, PMID:18245294) are real, complemented
requirements but downstream of secreted protease activity, so
KEEP_AS_NON_CORE rather than core.

Decisions summary

ACCEPT (8): GO:0006508 proteolysis (IBA, IDA seed, IEA); GO:0004222
metalloendopeptidase activity (IEA); GO:0005576 extracellular region (IEA and
three EXP rows).
MODIFY (2): both GO:0004175 endopeptidase activity rows ->
GO:0004222 metalloendopeptidase activity (specific descendant already carried
by the gene; metal dependence established structurally).
MARK_AS_OVER_ANNOTATED (2): GO:0015628, GO:0043952 (cargo, not machinery),
each with a PseudoCAP source defect.
KEEP_AS_NON_CORE (2): GO:0044010 single-species biofilm formation,
GO:0071978 swarming motility.
NEW (3): GO:0008270 zinc ion binding and GO:0005509 calcium ion binding (IDA,
PMID:1899664, mapped ligands in PDB 1EZM); GO:0016540 protein autoprocessing
(IMP, PMID:1744034 — LasB cleaves its own 197/198 bond, so it does the work).
No REMOVE.