Baseplate central spike protein and tail-associated peptidoglycan hydrolase (gp5) of bacteriophage T4 that forms a heterotrimeric (gp27-gp5)3 cell-puncturing complex at the distal hub of the contractile tail baseplate. Synthesized as a 575-residue precursor with an N-terminal gp27-binding OB-fold domain, a central N-acetylmuramidase (lysozyme) domain, and a C-terminal triple-stranded beta-helix needle domain, gp5 is proteolytically cleaved between Ser351 and Ala352 during morphogenesis into mature gp5* and gp5C fragments that remain associated in the virion. Upon tail sheath contraction, the C-terminal beta-helix needle punctures the host outer membrane and dissociates to relieve autoinhibition of the lysozyme domain, which locally digests the periplasmic peptidoglycan layer to allow tail tube penetration and viral DNA injection.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003796 lysozyme activity | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation correctly captures the N-acetylmuramidase activity of the central lysozyme domain of gp5. Reason: The middle domain of gp5 (residues 174-339) is a canonical T4-type N-acetylmuramidase (EC 3.2.1.17) that cleaves beta-1,4-glycosidic linkages between N-acetylmuramic acid and N-acetylglucosamine in host peptidoglycan. Supporting Evidence: file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. file:BPT4/5/5-uniprot.txt Baseplate central spike complex-associated lysozyme that is essential for the localized hydrolysis of bacterial cell wall, so that the tail tube, through which the phage DNA is ejected, can penetrate to the host inner membrane |
| GO:0003824 catalytic activity | IEA GO_REF:0000043 | MODIFY | Summary: Keyword-based annotation is correct in principle but overly general compared to the experimentally established lysozyme activity. Reason: The specific enzymatic activity of gp5 is peptidoglycan N-acetylmuramidase (lysozyme) activity (GO:0003796), which is already directly annotated to this gene product. Proposed replacements: lysozyme activity Supporting Evidence: file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. |
| GO:0009253 peptidoglycan catabolic process | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation accurately reflects the localized enzymatic degradation of host peptidoglycan by gp5 during phage entry. Reason: The central lysozyme domain of gp5 directly hydrolyzes the periplasmic peptidoglycan layer of the Escherichia coli cell wall during infection. Supporting Evidence: file:BPT4/5/5-deep-research-falcon.md T4 gp5 contains a **lysozyme-like muramidase domain** (EC **3.2.1.17**, N-acetylmuramidase). Experimental literature summarized by Moak & Molineux reports that gp5 βhas been shown to have the same substrate specificity as the gpE lysozyme,β and the lysozyme reaction is cleavage of the **Ξ²-1,4 glycosidic bond between NAM and NAG** in peptidoglycan. PMID:3157805 We assume that the tail-lysozyme plays an essential role in locally digesting the peptidoglycan layer to let the tube penetrate into the periplasmic space. |
| GO:0016787 hydrolase activity | IEA GO_REF:0000043 | MODIFY | Summary: Broad keyword-derived molecular function term that should be refined to lysozyme activity. Reason: While gp5 is a hydrolase, its precise catalytic function is well characterized as lysozyme activity (GO:0003796). Proposed replacements: lysozyme activity Supporting Evidence: file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. |
| GO:0016798 hydrolase activity, acting on glycosyl bonds | IEA GO_REF:0000043 | MODIFY | Summary: Correct parent glycosidase term from keyword mapping, but less specific than lysozyme activity. Reason: The glycosyl bond hydrolase activity of gp5 is specifically N-acetylmuramidase / lysozyme activity (GO:0003796). Proposed replacements: lysozyme activity Supporting Evidence: file:BPT4/5/5-deep-research-falcon.md T4 gp5 contains a **lysozyme-like muramidase domain** (EC **3.2.1.17**, N-acetylmuramidase). Experimental literature summarized by Moak & Molineux reports that gp5 βhas been shown to have the same substrate specificity as the gpE lysozyme,β and the lysozyme reaction is cleavage of the **Ξ²-1,4 glycosidic bond between NAM and NAG** in peptidoglycan. |
| GO:0016998 cell wall macromolecule catabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro-derived process term is correct but more general than peptidoglycan catabolic process. Reason: The cell wall macromolecule degraded by gp5 is specifically bacterial peptidoglycan, captured by GO:0009253 (peptidoglycan catabolic process) and in the context of viral entry by GO:0098932. Proposed replacements: peptidoglycan catabolic process Supporting Evidence: file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. |
| GO:0031640 killing of cells of another organism | IEA GO_REF:0000043 | REMOVE | Summary: Spurious keyword-based mapping from bacteriolytic/antimicrobial lysozyme keywords that does not reflect the biological role of the virion-associated tail spike lysozyme. Reason: Unlike soluble antimicrobial lysozymes or the phage endolysin gpE (which lyses the bacterial host at the end of the replication cycle), virion-associated gp5 performs strictly localized puncturing and peptidoglycan hydrolysis to allow tail tube penetration and genome injection into a viable host cell. Supporting Evidence: file:BPT4/5/5-uniprot.txt Baseplate central spike complex-associated lysozyme that is essential for the localized hydrolysis of bacterial cell wall, so that the tail tube, through which the phage DNA is ejected, can penetrate to the host inner membrane file:BPT4/5/5-deep-research-falcon.md T4 gp5 contains a **lysozyme-like muramidase domain** (EC **3.2.1.17**, N-acetylmuramidase). Experimental literature summarized by Moak & Molineux reports that gp5 βhas been shown to have the same substrate specificity as the gpE lysozyme,β and the lysozyme reaction is cleavage of the **Ξ²-1,4 glycosidic bond between NAM and NAG** in peptidoglycan. |
| GO:0042742 defense response to bacterium | IEA GO_REF:0000043 | REMOVE | Summary: Inappropriate automated keyword mapping from UniProt Antimicrobial keyword onto a bacteriophage entry protein. Reason: Bacteriophage T4 is a bacterial virus infecting its Escherichia coli host rather than a multicellular host mounting an immune or defense response against a bacterium. Supporting Evidence: file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. |
| GO:0046718 symbiont entry into host cell | IEA GO_REF:0000043 | MODIFY | Summary: Correct biological process term, but less specific than the child term for entry via peptidoglycan disruption. Reason: The specific mechanism of gp5-mediated entry is captured by the descendant term GO:0098932 (symbiont entry into host cell via disruption of host cell wall peptidoglycan). Proposed replacements: symbiont entry into host cell via disruption of host cell wall peptidoglycan Supporting Evidence: file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. |
| GO:0098003 viral tail assembly | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation correctly captures the essential structural role of gp5 in baseplate hub and tail morphogenesis. Reason: The (gp27-gp5)3 central spike complex is an essential structural core of the baseplate hub around which the six baseplate wedges and tail tube assemble. Supporting Evidence: file:BPT4/5/5-deep-research-falcon.md In T4, the central puncturing device is formed by a **(gp27βgp5*βgp5C)3** complex, which aligns with and extends the tail tube to form a penetration and DNA-translocation path. PMID:10217762 Tail-associated lysozyme of bacteriophage T4 (tail lysozyme), the product of gene 5 (gp 5), is an essential structural component of the hub of the phage baseplate. |
| GO:0098015 virus tail | IEA GO_REF:0000120 | MODIFY | Summary: Broad cellular component term that should be refined to the specific baseplate subcompartment. Reason: Within the virion tail, gp5 localizes specifically to the central spike hub of the baseplate (GO:0098025). Proposed replacements: virus tail, baseplate Supporting Evidence: file:BPT4/5/5-uniprot.txt The central spike complex, which creates an extension of the tail tube, is made up of three copies of the gp27-gp5*-gp5C complex and one copy of gp5.4 file:BPT4/5/5-deep-research-falcon.md In T4, the central puncturing device is formed by a **(gp27βgp5*βgp5C)3** complex, which aligns with and extends the tail tube to form a penetration and DNA-translocation path. |
| GO:0098025 virus tail, baseplate | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation accurately places gp5 in the viral tail baseplate. Reason: Three copies of gp5 form the central spike of the bacteriophage T4 baseplate hub. Supporting Evidence: file:BPT4/5/5-uniprot.txt The central spike complex, which creates an extension of the tail tube, is made up of three copies of the gp27-gp5*-gp5C complex and one copy of gp5.4 file:BPT4/5/5-deep-research-falcon.md In T4, the central puncturing device is formed by a **(gp27βgp5*βgp5C)3** complex, which aligns with and extends the tail tube to form a penetration and DNA-translocation path. |
| GO:0098932 symbiont entry into host cell via disruption of host cell wall peptidoglycan | IEA GO_REF:0000120 | ACCEPT | Summary: Automated annotation precisely describes the biological role of gp5 during bacteriophage T4 entry. Reason: During infection, gp5 punctures the outer membrane and hydrolyzes the host peptidoglycan layer so the tail tube can traverse the periplasm for DNA injection. Supporting Evidence: file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. file:BPT4/5/5-uniprot.txt Baseplate central spike complex-associated lysozyme that is essential for the localized hydrolysis of bacterial cell wall, so that the tail tube, through which the phage DNA is ejected, can penetrate to the host inner membrane |
| GO:0098994 symbiont entry into host cell via disruption of host cell envelope | IEA GO_REF:0000043 | MODIFY | Summary: Correct parent process term that should be refined to the specific peptidoglycan-disrupting entry term. Reason: The more specific child term GO:0098932 (symbiont entry into host cell via disruption of host cell wall peptidoglycan) is already present and directly captures the enzymatic mechanism of gp5. Proposed replacements: symbiont entry into host cell via disruption of host cell wall peptidoglycan Supporting Evidence: file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. |
| GO:0003796 lysozyme activity | EXP PMID:10217762 The C-terminal fragment of the precursor tail lysozyme of ba... | ACCEPT | Summary: Experimental characterization confirms the lysozyme activity of recombinant and mature gp5. Reason: Kanamaru et al. (1999) overexpressed and purified gp5, demonstrating muramidase activity of both the precursor/nicked complex and the isolated mature N-terminal gp5* fragment. Supporting Evidence: PMID:10217762 The lysozyme activity of the precursor or the nicked protein is about 10% of that of mature gp 5. file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. |
| GO:0005515 protein binding | IPI PMID:11823865 Structure of the cell-puncturing device of bacteriophage T4. | MODIFY | Summary: Crystal structure of the (gp5-gp27)3 complex demonstrates that gp5 and gp27 co-assemble as structural constituents of the virion baseplate hub spike. Reason: Bare GO:0005515 (protein binding) is uninformative; the 2.9 A crystal structure of the (gp5-gp27)3 cell-puncturing complex (PMID:11823865) specifically establishes gp5 as a structural constituent of the virion baseplate central spike (GO:0039660). Proposed replacements: structural constituent of virion Supporting Evidence: PMID:11823865 The amino-terminal, antiparallel beta-barrel domain of gp5 is inserted into a cylinder formed by three gp27 monomers, which may serve as a channel for DNA ejection. file:BPT4/5/5-deep-research-falcon.md In T4, the central puncturing device is formed by a **(gp27βgp5*βgp5C)3** complex, which aligns with and extends the tail tube to form a penetration and DNA-translocation path. |
| GO:0003796 lysozyme activity | IMP PMID:15701513 Control of bacteriophage T4 tail lysozyme activity during th... | ACCEPT | Summary: Mutational and structural analysis of the Ser351-Ala352 cleavage site demonstrates how maturation cleavage controls gp5 lysozyme activity. Reason: Kanamaru et al. (2005) characterized cleavage-site mutants and showed that autoinhibition of the gp5 lysozyme domain by an adjacent monomer's linker loop is relieved upon dissociation of the C-terminal beta-helix. Supporting Evidence: PMID:15701513 The lysozyme activity is inhibited in the wild-type structure by a loop from the adjacent gp5 monomer that binds into the substrate-binding site. file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. |
| GO:0005515 protein binding | IPI PMID:15701513 Control of bacteriophage T4 tail lysozyme activity during th... | MODIFY | Summary: Co-crystallization of the gp5 S351L mutant with gp27 confirms its role as a structural subunit of the virion central spike complex. Reason: Bare GO:0005515 (protein binding) carries no specific functional information; the co-crystal structure with gp27 (PMID:15701513) characterizes gp5 as a structural constituent of the virion baseplate hub (GO:0039660). Proposed replacements: structural constituent of virion Supporting Evidence: PMID:15701513 The crystal structure of the non-cleavage phenotype mutant of gp5, S351L, complexed with gene product 27, showed that the 18 residues in the vicinity of the potential cleavage site (disordered in the wild-type structure) had visible electron density. file:BPT4/5/5-deep-research-falcon.md In T4, the central puncturing device is formed by a **(gp27βgp5*βgp5C)3** complex, which aligns with and extends the tail tube to form a penetration and DNA-translocation path. |
| GO:0042802 identical protein binding | IPI PMID:15701513 Control of bacteriophage T4 tail lysozyme activity during th... | KEEP AS NON CORE | Summary: Homotrimerization of gp5 via its C-terminal intertwined beta-helix and inter-monomer regulatory loop contacts is structurally verified. Reason: Three gp5 monomers assemble into a tightly intertwined trimer; retained as a non-core binding term. Supporting Evidence: PMID:15701513 The lysozyme activity is inhibited in the wild-type structure by a loop from the adjacent gp5 monomer that binds into the substrate-binding site. file:BPT4/5/5-deep-research-falcon.md In T4, the central puncturing device is formed by a **(gp27βgp5*βgp5C)3** complex, which aligns with and extends the tail tube to form a penetration and DNA-translocation path. |
| GO:0046718 symbiont entry into host cell | IMP PMID:15701513 Control of bacteriophage T4 tail lysozyme activity during th... | MODIFY | Summary: Complementation assays with non-cleavable gp5 mutants demonstrate its essential role in host entry, which is more specifically captured by GO:0098932. Reason: Refine to the specific child term GO:0098932 (symbiont entry into host cell via disruption of host cell wall peptidoglycan). Proposed replacements: symbiont entry into host cell via disruption of host cell wall peptidoglycan Supporting Evidence: PMID:15701513 The gp5 needle punctures the outer cell membrane and then digests the peptidoglycan cell wall in the periplasmic space. file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. |
| GO:0098015 virus tail | IMP PMID:15701513 Control of bacteriophage T4 tail lysozyme activity during th... | MODIFY | Summary: Localization to the viral tail is correct but less specific than virus tail, baseplate. Reason: Refine to GO:0098025 (virus tail, baseplate), where the (gp27-gp5)3 central spike resides. Proposed replacements: virus tail, baseplate Supporting Evidence: PMID:15701513 Its gene product 5 (gp5) has a needle-like structure attached to the end of a tube through which the DNA passes on its way out of the head and into the host. file:BPT4/5/5-deep-research-falcon.md In T4, the central puncturing device is formed by a **(gp27βgp5*βgp5C)3** complex, which aligns with and extends the tail tube to form a penetration and DNA-translocation path. |
| GO:0098025 virus tail, baseplate | IDA PMID:27193680 Structure of the T4 baseplate and its function in triggering... | ACCEPT | Summary: Near-atomic cryo-EM reconstruction of the T4 baseplate directly resolves the (gp27-gp5*-gp5C)3 central spike complex in the baseplate hub. Reason: Taylor et al. (2016) resolved the complete baseplate assembly, including the central spike formed by gp5 and gp27. Supporting Evidence: PMID:27193680 Here we present the atomic structure of the approximately 6-megadalton bacteriophage T4 baseplate in its pre- and post-host attachment states and explain the events that lead to sheath contraction in atomic detail. file:BPT4/5/5-uniprot.txt The central spike complex, which creates an extension of the tail tube, is made up of three copies of the gp27-gp5*-gp5C complex and one copy of gp5.4 file:BPT4/5/5-deep-research-falcon.md In T4, the central puncturing device is formed by a **(gp27βgp5*βgp5C)3** complex, which aligns with and extends the tail tube to form a penetration and DNA-translocation path. |
| GO:0003796 lysozyme activity | IDA PMID:3157805 Isolation and characterization of the bacteriophage T4 tail-... | ACCEPT | Summary: Classical biochemical isolation of tail-associated gp5 directly demonstrated its N-acetylmuramidase activity. Reason: Nakagawa et al. (1985) purified the tail-associated lysozyme from T4 tails, identified it as gp5, and demonstrated its N-acetylmuramidase activity with a pH optimum around 5.8. Supporting Evidence: PMID:3157805 The tail-lysozyme has N-acetylmuramidase activity and the same substrate specificity as gene e lysozyme; the optimum pH is around 5.8, about 1 pH unit lower than for the e lysozyme. file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. |
| GO:0044409 symbiont entry into host | IDA PMID:3157805 Isolation and characterization of the bacteriophage T4 tail-... | MODIFY | Summary: Broad entry annotation from classical characterization that should be refined to GO:0098932. Reason: Refine to the specific child term GO:0098932 (symbiont entry into host cell via disruption of host cell wall peptidoglycan). Proposed replacements: symbiont entry into host cell via disruption of host cell wall peptidoglycan Supporting Evidence: PMID:3157805 We assume that the tail-lysozyme plays an essential role in locally digesting the peptidoglycan layer to let the tube penetrate into the periplasmic space. file:BPT4/5/5-deep-research-falcon.md During adsorption-triggered tail contraction, the gp5 C-terminal Ξ²-helix needle is driven into the host envelope, while gp5βs lysozyme-like domain (muramidase; EC 3.2.1.17) locally cleaves peptidoglycan (NAMβNAG Ξ²(1β4) linkage) to facilitate tail tube penetration and DNA injection. |
Loading supporting contentβ¦
Download this section (compressed HTML)Q: Is the maturation cleavage of gp5 between Ser351 and Ala352 catalyzed autocatalytically within the (gp27-gp5)3 hub complex or by a specific host or phage protease during assembly?
Suggested experts: Shuji Kanamaru, Fumio Arisaka, Petr G. Leiman
Q: What is the exact fate of the dissociated gp5C beta-helix needle in the host periplasm or inner membrane during tail tube penetration and DNA translocation?
Suggested experts: Petr G. Leiman, Nicholas M. I. Taylor
Experiment: Perform cryo-electron tomography of bacteriophage T4 infecting Escherichia coli minicells using non-cleavable gp5(S351L) versus wild-type virions to visualize where envelope penetration stalls when gp5C cannot dissociate from gp5*.
Hypothesis: Virions carrying uncleaved gp5(S351L) will puncture the outer membrane upon sheath contraction but remain stalled at the peptidoglycan layer due to persistent autoinhibition of the lysozyme active site and steric blockage of the tail tube tip.
Type: Cryo-electron tomography of phage-infected minicells
Experiment: Use time-resolved hydrogen-deuterium exchange mass spectrometry (HDX-MS) on purified (gp27-gp5*-gp5C)3 complexes upon thermal or mechanical release of gp5C to map conformational changes in the linker loop (residues 340-388) and lysozyme active site.
Hypothesis: Dissociation of the gp5C beta-helix triggers a cooperative order-to-disorder transition in the inhibitory linker loop, exposing the catalytic cleft of gp5* for peptidoglycan binding.
Type: Hydrogen-deuterium exchange mass spectrometry (HDX-MS)
Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)