PP_2320 is a Sec-exported, periplasmic YkuD-family L,D-transpeptidase with LysM and catalytic domains. It is predicted to covalently anchor the major outer-membrane lipoprotein OprI to a peptidoglycan stem, coupling the outer membrane to the cell-wall sacculus.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000270 peptidoglycan metabolic process | IEA GO_REF:0000117 | ACCEPT | Summary: PP_2320 modifies a peptidoglycan stem while forming the OprI tether. Reason: The L,D-transpeptidase reaction directly remodels the peptide component of peptidoglycan. |
| GO:0004180 carboxypeptidase activity | IEA GO_REF:0000117 | REMOVE | Summary: OprI anchoring is an acyl-transfer reaction rather than terminal hydrolysis by a carboxypeptidase. Reason: The closely matched ErfK/LdtPae2 subfamily resolves the YkuD reaction as lipoprotein-acceptor L,D-transpeptidation. |
| GO:0005576 extracellular region | IEA GO_REF:0000118 | MODIFY | Summary: The signal peptide exports PP_2320 from the cytoplasm, but its peptidoglycan substrate is in the periplasm. Reason: In a Gram-negative bacterium, the periplasm is the precise compartment for an enzyme acting on the sacculus beneath the outer membrane. Proposed replacements: outer membrane-bounded periplasmic space |
| GO:0008360 regulation of cell shape | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: Outer-membrane tethering can affect envelope mechanics but does not establish a direct shape-regulatory role. Reason: The supported direct process is peptidoglycan-protein cross-linking. |
| GO:0016740 transferase activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: The root transferase term is true but uninformative for an L,D-transpeptidase. Reason: GO:0071972 already captures the specific catalytic class. |
| GO:0018104 peptidoglycan-protein cross-linking | IEA GO_REF:0000118 | ACCEPT | Summary: PP_2320 is assigned to covalent OprI anchoring at the peptidoglycan sacculus. Reason: Its exact PANTHER subfamily matches the experimentally characterized Pseudomonas LdtPae2/ErfK anchoring enzyme. Supporting Evidence: PMID:37255442 We found that the three P. aeruginosa LDTs catalyze peptidoglycan cross-linking (LdtPae1), the anchoring of lipoprotein OprI to the peptidoglycan (LdtPae2), and the hydrolysis of the resulting peptidoglycan-OprI amide bond (LdtPae3). |
| GO:0071555 cell wall organization | IEA GO_REF:0000104 | ACCEPT | Summary: Covalent coupling of OprI to peptidoglycan organizes the Gram-negative cell envelope. Reason: The reaction links an outer-membrane structural protein to the cell-wall scaffold. |
| GO:0071972 peptidoglycan L,D-transpeptidase activity | IEA GO_REF:0000118 | ACCEPT | Summary: PP_2320 is an intact YkuD-family L,D-transpeptidase specialized for a lipoprotein acceptor. Reason: The catalytic YkuD domain and exact ErfK-related PANTHER subfamily support this reaction class. |
| GO:0009252 peptidoglycan biosynthetic process | IEA GO_REF:0000041 | REMOVE | Summary: The reaction is a late peptidoglycan-envelope maturation event rather than glycan or stem synthesis. Reason: Covalent OprI anchoring modifies an existing sacculus and does not synthesize peptidoglycan glycan or stem material; GO:0018104 captures the direct process. |
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Gap: PP_2320 substrate specificity and physiological importance have not been tested directly in KT2440.
OPEN BIOLOGYCURATION
Significance: PA2854 OprI anchoring is established in vivo and in vitro, but transfer to the close PP_2320 ortholog remains untested in KT2440.
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