Endolysin (protein P15) of the lipid-containing, broad-host-range tectivirus bacteriophage PRD1, a 149-residue, 17.3 kDa glycosyl hydrolase family 24 enzyme encoded by gene XV. P15 is a beta-1,4-N-acetylmuramidase (lysozyme, EC 3.2.1.17) that hydrolyses the glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine in bacterial peptidoglycan. Its principal role is in the terminal, lytic stage of infection: acting together with the phage holin P35, which permeabilizes the host cytoplasmic membrane and allows the endolysin to reach the murein sacculus, P15 degrades the host cell wall, lysing the cell and releasing progeny virions. P15 is additionally a minor structural component of the virion, where it is peripherally associated with the internal phage membrane in a manner dependent on the small integral membrane proteins P20 and P22. It is not, however, the muralytic enzyme responsible for penetrating the peptidoglycan during genome entry: that role belongs to the separate PRD1 protein P7, and P15-deficient particles initiate DNA replication normally.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003796 lysozyme activity | EXP PMID:11741849 The lytic enzyme of bacteriophage PRD1 is associated with th... | ACCEPT | Summary: Zymogram and turbidimetric assays of purified wild-type and amber-mutant PRD1 particles attribute a ~15 kDa muralytic activity to P15, absent from all three gene XV amber mutants. Reason: This is the gene's demonstrated catalytic activity, matching EC 3.2.1.17. In PMID:11741849 the faster-migrating clear zone in peptidoglycan zymograms is lost in sus174, sus232 and sus240 (P15-) particles and its mass matches P15, and the activity is also detected in isolated phage membranes. The same activity is what UniProt curates as the entry's catalytic activity. Supporting Evidence: PMID:11741849 Thus, we concluded that the appearance of the faster-moving clear zone in zymograms was due to the enzymatic activity of protein P15. PMID:11741849 Protein P15 is a soluble beta-1,4-N-acetylmuramidase that causes phage-induced host cell lysis. file:BPPRD/XV/XV-uniprot.txt Reaction=Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins. |
| GO:0003796 lysozyme activity | IDA PMID:10931330 Bacteriophage PRD1 DNA entry uses a viral membrane-associate... | ACCEPT | Summary: CACAO row. The claim is right and independently established, but the cited paper is principally about a different PRD1 protein: it characterises the glycolytic activity of P7, the virion-associated lytic transglycosylase, and maps the P14 reading frame. Reason: CACAO assignment, experimental (IDA). The term is correct for this gene - lysozyme activity is established for P15 by PMID:7925454 and PMID:11741849 - so the annotation is accepted and the curator deferred to. The reference choice is nonetheless the weak point, and is flagged as MISCITED in reference_review: PMID:10931330 attributes the activity it analyses to P7, and its conclusion concerns P7 and P14 forming a heteromultimeric complex at the particle vertices. Its zymograms of wild-type and mutant particles do also contain a second, faster-migrating muralytic zone, which PMID:11741849 subsequently identified as P15 while revisiting exactly these zymograms, so a figure-level reading by the student may well be sound. This could not be checked: the cached record is abstract-only (full_text_available: false) and the GONUTS wiki page for this PMID, which would record the student's evidence, was offline when queried (2026-10-29). No REMOVE, per the curator-deference rule; the appropriate upstream fix, if the full text has no P15-specific panel, is to re-reference the row to PMID:7925454 rather than drop the claim. Supporting Evidence: PMID:11741849 Protein P15 is a soluble beta-1,4-N-acetylmuramidase that causes phage-induced host cell lysis. PMID:11741849 The zone that moved more slowly was identified previously as protein P7, which has a conserved lytic transglycosylase domain in its N-terminal half |
| GO:0003796 lysozyme activity | IDA PMID:7925454 Gene XV of bacteriophage PRD1 encodes a lytic enzyme with mu... | ACCEPT | Summary: CACAO row on the primary characterisation paper: recombinant P15 purified to near homogeneity cleaves the beta-1,4 MurNAc-GlcNAc bond of peptidoglycan, i.e. lysozyme activity (EC 3.2.1.17). Reason: CACAO assignment, experimental (IDA), and the term matches what the paper shows for this gene exactly. PMID:7925454 clones gene XV, purifies P15, confirms its identity by N-terminal sequencing, measures turbidimetric lysis of chloroform-treated Gram-negative cells, and determines the bond specificity from cell-wall digest analysis. GO:0003796 is the EC 3.2.1.17-equivalent term and is the right granularity for that chemistry; no downstream phenotype is being read as an activity here. Supporting Evidence: PMID:7925454 The analysis of cell wall digests indicated that P15 is a glycosidase that cleaves the beta (1-4) linkage between N-acetylmuramic acid and N-acetylglucosamine, thus displaying muramidase activity. PMID:7925454 The purified protein P15, identified by N-terminal sequence analysis, showed a strong lytic activity against chloroform-treated Gram-negative cells. |
| GO:0003796 lysozyme activity | IEA GO_REF:0000003 | ACCEPT | Summary: Electronic mapping from EC 3.2.1.17, the EC number UniProt assigns to this entry on experimental evidence from PMID:7925454 and PMID:11741849. Reason: The EC-to-GO mapping is correct and, unusually for an IEA, its input is itself experimentally grounded: the EC number on this entry carries ECO:0000269 evidence from the two characterisation papers, and the curated reaction is precisely the MurNAc-GlcNAc beta-1,4 hydrolysis demonstrated in PMID:7925454. This row therefore reinforces the experimental rows for the same term rather than duplicating an unverified prediction. Supporting Evidence: PMID:7925454 The analysis of cell wall digests indicated that P15 is a glycosidase that cleaves the beta (1-4) linkage between N-acetylmuramic acid and N-acetylglucosamine, thus displaying muramidase activity. file:BPPRD/XV/XV-uniprot.txt Reaction=Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins. |
| GO:0003824 catalytic activity | IEA GO_REF:0000043 | TOO GENERAL | Summary: Root-level catalytic activity from the Bacteriolytic enzyme keyword. True but entailed by the accepted glycosidase terms. Reason: GO:0003824 is an ancestor of GO:0003796 and GO:0033922, both of which are accepted in this review on direct experimental evidence. The claim is not false, merely uninformative once the specific hydrolase activity is asserted. Supporting Evidence: PMID:7925454 The analysis of cell wall digests indicated that P15 is a glycosidase that cleaves the beta (1-4) linkage between N-acetylmuramic acid and N-acetylglucosamine, thus displaying muramidase activity. |
| GO:0016787 hydrolase activity | IEA GO_REF:0000043 | TOO GENERAL | Summary: Hydrolase activity from the Hydrolase keyword; an ancestor of the accepted specific glycosidase terms. Reason: Correct - P15 is a hydrolase - but GO:0016787 is subsumed by GO:0003796 and GO:0033922, which this review accepts from direct assays of the cleaved bond. Supporting Evidence: PMID:7925454 The analysis of cell wall digests indicated that P15 is a glycosidase that cleaves the beta (1-4) linkage between N-acetylmuramic acid and N-acetylglucosamine, thus displaying muramidase activity. |
| GO:0016798 hydrolase activity, acting on glycosyl bonds | IEA GO_REF:0000043 | TOO GENERAL | Summary: Glycosidase-level term from the Glycosidase keyword; an ancestor of both accepted specific terms. Reason: The glycosidase assignment is right, and the keyword is well founded, but GO:0016798 is an ancestor of GO:0003796 and GO:0033922 and adds nothing once the bond specificity is annotated. Supporting Evidence: file:BPPRD/XV/XV-uniprot.txt Belongs to the glycosyl hydrolase 24 family. |
| GO:0031640 killing of cells of another organism | IEA GO_REF:0000043 | TOO GENERAL | Summary: Keyword-derived host-killing term. P15 does kill the host cell, but the specific term for how and why - viral release from host cell by cytolysis - is accepted below and sits under this one. Reason: GO:0044659 (accepted) is a descendant of GO:0031640 via symbiont-mediated cytolysis of host cell. The broad term is true of P15 but uninformative once the cytolytic-release term is asserted, and it loses the point that the killing is the mechanism of progeny release rather than an antibacterial effect in its own right. Supporting Evidence: PMID:16030234 Using infected cells and plasmid-borne lysis genes, we demonstrated that a two-component lysis system (holin-endolysin) operates to release progeny phage particles from the host cell. |
| GO:0033922 peptidoglycan beta-N-acetylmuramidase activity | IDA PMID:7925454 Gene XV of bacteriophage PRD1 encodes a lytic enzyme with mu... | ACCEPT | Summary: CACAO row. Cell-wall digest analysis of purified recombinant P15 identifies it as a beta-N-acetylmuramidase acting on peptidoglycan - exactly what this term denotes. Reason: CACAO assignment, experimental (IDA), and the term matches the assay closely. The paper's own title and conclusion name muramidase activity, and the digest analysis fixes the hydrolysed bond. GO:0033922 is a sibling of GO:0003796 rather than a descendant of it (both lie under GO:0004553), so the two rows are two complementary names for the same demonstrated chemistry, not a granularity conflict; GO:0033922 is the more explicit about the peptidoglycan substrate, GO:0003796 the EC-equivalent. Both are kept. Whether GO should hold two terms for one EC number is an ontology question, raised in suggested_questions. Supporting Evidence: PMID:7925454 The analysis of cell wall digests indicated that P15 is a glycosidase that cleaves the beta (1-4) linkage between N-acetylmuramic acid and N-acetylglucosamine, thus displaying muramidase activity. PMID:11741849 Protein P15 is a soluble beta-1,4-N-acetylmuramidase that causes phage-induced host cell lysis. |
| GO:0042742 defense response to bacterium | IEA GO_REF:0000043 | REMOVE | Summary: Keyword KW-0081 (Antimicrobial) mapped to a host-defence process term. The direction of the interaction is inverted: PRD1 is the attacker of the bacterium, not an organism defending itself against one. Reason: GO:0042742 denotes a reaction mounted to protect the annotated organism from a bacterium. A phage endolysin degrades the peptidoglycan of its own host in order to release progeny virions; there is no defence, and no bacterium is being resisted by PRD1. This is a demonstrably wrong electronic keyword-to-GO mapping - the Antimicrobial keyword is applied both to host antimicrobial peptides and to phage lysis enzymes, and only the former fits the defence framing - which the guidelines list as legitimate ground for REMOVE. The real claim behind the keyword is already carried, correctly, by GO:0031640 and GO:0044659. Worth reporting upstream as a keyword-mapping defect affecting phage-encoded lytic enzymes generally. Supporting Evidence: file:BPPRD/XV/XV-uniprot.txt Endolysin involved in host peptidoglycan digestion after permeabilization of the cytoplasmic membrane by holin. Involved in host cell lysis and liberation of progeny phages. |
| GO:0044277 cell wall disassembly | IDA PMID:7925454 Gene XV of bacteriophage PRD1 encodes a lytic enzyme with mu... | MODIFY | Summary: CACAO row. The assay - digestion of bacterial cell walls by purified P15 - is right, but GO:0044277 is a cellular process term for an organism taking apart its own cell wall, which a phage protein acting on its host's sacculus is not. Reason: CACAO assignment, experimental (IDA), and the paper genuinely shows cell-wall degradation by this gene product: P15 lyses chloroform-treated Gram-negative cells and its digests reveal cleavage of the MurNAc-GlcNAc bond. So the substance is supported. The term is the wrong one in sense, not in strength: GO:0044277 sits under cellular process and cell wall organization, describing the breakdown of the annotated organism's own wall, whereas PRD1 has no cell wall at all and P15 acts across a species boundary. GO has the matching host-directed term, GO:0052009 symbiont-mediated disruption of host cell wall, under the interspecies-interaction branch. Replacing the term keeps the student's observation and places it in the right branch. This is a recurring risk for phage and pathogen proteins: a process term that is structurally correct but chosen without its taxon-directed counterpart. Proposed replacements: symbiont-mediated disruption of host cell wall Supporting Evidence: PMID:7925454 The purified protein P15, identified by N-terminal sequence analysis, showed a strong lytic activity against chloroform-treated Gram-negative cells. PMID:7925454 The analysis of cell wall digests indicated that P15 is a glycosidase that cleaves the beta (1-4) linkage between N-acetylmuramic acid and N-acetylglucosamine, thus displaying muramidase activity. file:BPPRD/XV/XV-uniprot.txt Endolysin involved in host peptidoglycan digestion after permeabilization of the cytoplasmic membrane by holin. |
| GO:0044659 viral release from host cell by cytolysis | IDA PMID:16030234 The Holin protein of bacteriophage PRD1 forms a pore for sma... | ACCEPT | Summary: CACAO row on the PRD1 lysis-system paper, which establishes a two-component holin-endolysin system releasing progeny phage, with P15 as the endolysin indispensable for lysis. Reason: CACAO assignment, experimental (IDA), and the term matches the paper's central result for this gene. PMID:16030234 shows that the gene XV amber mutant sus232 does not lyse, with or without arsenate (Fig. 1B), and separates the two proteins' contributions by plasmid-borne expression: holin alone gives potassium leakage and membrane-voltage loss but no lysis, endolysin alone gives neither, and only coexpression lyses the culture (Fig. 5). That is participation, not mere necessity - P15 performs the peptidoglycan hydrolysis step that ruptures the cell - and the cytolytic release of virions is the process that step serves. Not a phenotype read as a process: the molecular step and the process term coincide here. Supporting Evidence: PMID:16030234 Using infected cells and plasmid-borne lysis genes, we demonstrated that a two-component lysis system (holin-endolysin) operates to release progeny phage particles from the host cell. PMID:16030234 The same result was observed in the case of the endolysin sus232 mutant. PMID:16030234 that endolysin was needed for cell lysis |
| GO:0044659 viral release from host cell by cytolysis | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from IPR016284, the PRD1 P15 lysozyme family signature. Reason: The signature is the family defined around this very protein, and the mapped process is the one experimentally demonstrated for it in PMID:16030234 and PMID:7925454. The electronic row agrees with the experimental one and needs no adjustment. Supporting Evidence: PMID:16030234 Using infected cells and plasmid-borne lysis genes, we demonstrated that a two-component lysis system (holin-endolysin) operates to release progeny phage particles from the host cell. file:BPPRD/XV/XV-uniprot.txt Involved in host cell lysis and liberation of progeny phages. |
| GO:0055036 virion membrane | IDA PMID:11741849 The lytic enzyme of bacteriophage PRD1 is associated with th... | KEEP AS NON CORE | Summary: CACAO row. P15 is a structural component of the PRD1 virion, peripherally associated with the internal phage membrane; supported by several independent assays, not a single image. Reason: CACAO assignment, experimental (IDA), and the term matches what the paper shows. This is not the single-assay localization pattern: PMID:11741849 detects P15 activity by zymography in capsid-free phage membrane vesicles and in both empty and DNA-filled GuHCl-released membranes (Fig. 3a), shows a roughly fivefold rise in particle-associated lytic activity when the capsid is partly dissociated by freeze-thaw, and makes the association dependent on the small integral membrane proteins P20 and P22 (Fig. 1, Fig. 2). UniProt curates the same location as virion membrane, peripheral membrane protein. It is kept as non-core rather than accepted because the enzyme's demonstrated role is in lysis from within the infected cell at the end of the cycle, whereas the virion-associated copy has no established function - P15-deficient particles initiate DNA replication on schedule, so packaged P15 is not the entry muralytic enzyme. The location is as precise as the evidence allows: the data place P15 on the membrane peripherally, probably near a vertex, but do not resolve a sub-structure. Supporting Evidence: PMID:11741849 We demonstrate here that P15 is also a structural component of the PRD1 virion and that it is connected to the phage membrane. PMID:11741849 Zymogram analysis revealed the presence of proteins P7 and P15 in both DNA-filled and empty phage membranes PMID:11741849 Small viral membrane proteins P20 and P22 modulate incorporation of P15 into the virion and may connect it to the phage membrane. file:BPPRD/XV/XV-uniprot.txt May be associated with the viral membrane via P20 and P22. |
| GO:0055036 virion membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Subcellular-location vocabulary mapping of the curated virion membrane location, which itself rests on PMID:11741849. Reason: The mapping is faithful to a curated, experimentally evidenced location (ECO:0000269 from PMID:11741849 in the UniProt entry), so it reinforces the experimental row for the same term. Kept as non-core for the same reason as that row: the virion-associated pool of P15 has no demonstrated function. Supporting Evidence: PMID:11741849 We demonstrate here that P15 is also a structural component of the PRD1 virion and that it is connected to the phage membrane. file:BPPRD/XV/XV-uniprot.txt May be associated with the viral membrane via P20 and P22. |
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Download this section (compressed HTML)Q: GO holds both GO:0003796 lysozyme activity (the EC 3.2.1.17-equivalent term) and GO:0033922 peptidoglycan beta-N-acetylmuramidase activity as siblings under GO:0004553, and PRD1 P15 carries both. Should they be merged, or is the intended distinction that GO:0003796 additionally covers chitodextrin hydrolysis?
Q: Does the UniProt Antimicrobial keyword (KW-0081) need splitting, or its GO mapping restricting, so that bacteriophage and plasmid lysis enzymes are no longer mapped to GO:0042742 defense response to bacterium?
Q: What, if anything, does the virion-associated copy of P15 do? It is packaged in a P20/P22-dependent manner and is enzymatically active in isolated phage membranes, yet its absence does not delay DNA entry; is it simply carried over for lysis in the next host, or does it contribute to penetrating the walls of the Gram-positive and more distant hosts of the tectiviruses?
Q: Is P15 the signal, or merely a neighbour of it, in the P2-dependent initiation of genome delivery? Particles supplied with P2 in trans but lacking P15 adsorb normally yet are compromised in initiating infection, which the authors read either as mispositioning of P2 or as a direct role for P15 in signalling.
Experiment: Construct and propagate a P7-/P15- double mutant (so far unobtainable) using suppressor hosts or trans-complementation, and assay genome entry kinetics, peptidoglycan penetration and infectivity against Gram-negative and Gram-positive tectivirus hosts.
Hypothesis: The two virion-associated muralytic enzymes are partially redundant for entry, with P15 providing the activity needed on Gram-positive or otherwise atypical peptidoglycan, which is why PRD1 carries both.
Experiment: Cryo-electron tomography with immunolabelling or activity-based labelling of wild-type, P20- and P22-deficient PRD1 particles to localise P15 within the virion, together with a quantitative measurement of copy number per particle.
Hypothesis: P15 occupies a defined, P20/P22-tethered site at or near the special vertex of the internal membrane rather than being distributed over the membrane.
Experiment: Reconstitute the holin-endolysin step in vitro with purified P35 in proteoliposomes and purified P15, measuring P15 translocation across the membrane and subsequent sacculus digestion as a function of membrane voltage and ATP level.
Hypothesis: P15 crosses the cytoplasmic membrane only through the collapsed, endolysin-permeable state of the holin complex, and the ATP drop seen in infected cells is what gates that transition.
Experiment: Determine the structure of P15 by crystallography or cryo-EM, using the AlphaFold model as a starting point, and test the predicted catalytic residues of the glycosyl hydrolase 24 fold by site-directed mutagenesis, assaying turbidimetric lysis, zymogram activity and the enzyme's thermal and ionic-strength lability.
Hypothesis: P15 adopts a GH24 phage-lysozyme fold whose catalytic machinery is conserved despite low sequence similarity, and its instability maps to a small number of surface or packing residues that can be engineered out.
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