XV (protein P15, endolysin) — Enterobacteria phage PRD1 (UniProt P13559)

Provenance note

Automated deep research was not available in this environment (no provider API
keys), so no -deep-research-<provider>.md file exists for this gene. These notes
were assembled by reading the cached publications in publications/, the UniProt
flat file XV-uniprot.txt, and PubMed searches. The GONUTS wiki
(gowiki.tamu.edu), which records the CACAO students' evidence per PMID, was
offline when queried on 2026-10-29 ("This site is temporarily offline while we
perform upgrades."), so the student-supplied evidence text could not be inspected
for the five CACAO rows.

Identity

• 149 aa protein, 17.3 kDa, encoded by PRD1 gene XV; also called P15, beta-1,4-N-acetylmuramidase, lysozyme, lytic enzyme PMID:2651121.
• Sequence is distinctive among lytic enzymes, with only weak local similarity to phage lysozymes PMID:2651121. UniProt places it in glycosyl hydrolase family 24 (ECO:0000305) and PIRSF001069 / Pfam PF11860 (Muramidase) / IPR016284 (Phage PRD1 P15 lysozyme).

Molecular function: muramidase (lysozyme)

• Recombinant P15 purified from an expression plasmid lyses chloroform-treated Gram-negative cells; cell-wall digest analysis establishes the bond specificity PMID:7925454.
• Same paper: purity and identity confirmed, lytic activity Gram-negative-selective, pH optimum 7.0–8.0 PMID:7925454.
• In virion zymograms P15 appears as a ~15 kDa clear zone absent from sus174, sus232, sus240 (P15-) and P20- particles PMID:11741849. Against Gram-positive (M. lysodeikticus) peptidoglycan, P15 (unlike P7) is active in zymograms PMID:11741849 — note this is in apparent contrast to the turbidimetric result of PMID:7925454 on intact Gram-positive cells, presumably an accessibility rather than specificity difference.
• UniProt records EC 3.2.1.17 with experimental evidence from both papers [file:BPPRD/XV/XV-uniprot.txt "Reaction=Hydrolysis of (1->4)-beta-linkages between N-acetylmuramic"].

Biological process: holin-dependent host lysis and progeny release

• PRD1 lyses its host with a canonical two-component holin (P35, gene XXXV) / endolysin (P15, gene XV) system PMID:16030234.
• Both proteins are required: neither the holin mutant sus715 nor the endolysin mutant sus232 lyses, with or without arsenate [PMID:16030234 "The same result was observed in the case of the endolysin sus232 mutant."; "These observations confirm that both the phage holin and endolysin proteins are necessary for premature lysis."].
• Plasmid-borne reconstruction separates the two activities: holin alone gives K+ leakage and loss of membrane voltage but no lysis; endolysin alone gives nothing; together they lyse PMID:16030234.
• So P15's own step is peptidoglycan hydrolysis from the cytoplasmic side after holin permeabilizes the membrane; the lysis and the release of progeny virions are the direct consequence [file:BPPRD/XV/XV-uniprot.txt "Endolysin involved in host peptidoglycan digestion after"].

Virion association (cellular component)

• P15 is not only a soluble lysis enzyme but a structural component of the virion, connected to the internal phage membrane PMID:11741849.
• Evidence is multi-pronged, not a single image: zymogram detection of P15 in isolated, capsid-free and GuHCl-released phage membrane vesicles, both empty and DNA-filled PMID:11741849; ~5-fold activation of particle-associated lytic activity on partial capsid dissociation by freeze–thaw; and dependence of particle-associated P15 activity on the small integral membrane proteins P20 and P22 PMID:11741849.
• UniProt: Virion membrane; peripheral membrane protein, possibly tethered via P20/P22 [file:BPPRD/XV/XV-uniprot.txt "Peripheral membrane protein {ECO:0000269|PubMed:11741849}. Note=May be"].

What P15 does not do: DNA entry

• The virion-entry muralytic role belongs to the P7 transglycosylase, not P15. P15- particles show no delay in initiating phage DNA replication PMID:11741849.
• PMID:10931330 is a paper about P7, not P15: it reports the P7-associated glycolytic activity in zymograms and maps P14 PMID:10931330. It carries a CACAO IDA row for GO:0003796 on P13559. Its zymograms of wild-type and mutant particles do also show the second, faster-moving muralytic zone later identified as P15 (PMID:11741849 revisits exactly these zymograms), so the annotation is plausible but the paper's own attribution is to P7; the cached record is abstract-only and the GONUTS page was offline, so this row is left UNDECIDED rather than removed (curator-deference rule).
• A secondary, non-enzymatic observation: P2+P15- particles adsorb normally but initiate infection poorly, prompting the speculation that P15 contributes to the DNA-delivery signal at the vertex PMID:11741849. This is explicitly speculative and is not annotated.

Notes on the IEA/keyword-derived rows

• GO:0042742 defense response to bacterium comes from keyword KW-0081 (Antimicrobial) via GO_REF:0000043. For a phage endolysin this reads a host-killing activity as a defense response of the annotated organism; the phage is the attacker, not a defender, and GO:0031640 killing of cells of another organism already carries the real claim. Over-annotation.
• GO:0003824 and GO:0016787 are ancestors of the asserted GO:0033922/GO:0003796; GO:0016798 likewise. True but entailed.
• GO:0044659 viral release from host cell by cytolysis (InterPro IPR016284 = the P15 family itself) matches the experimental picture exactly.