Exonuclease subunit 1 (gp47) is the 339-amino-acid Mre11-family metallophosphoesterase nuclease subunit of the bacteriophage T4 Mre11-Rad50 (gp47-gp46) DNA end-processing complex. Partnering with the Rad50-like ABC-type ATPase subunit gp46 in a heterotetrameric assembly, gp47 catalyzes metal-dependent single-stranded DNA endonuclease and ATP-stimulated double-stranded DNA exonuclease activities that resect DNA ends to generate 3' single-stranded DNA tails. Interaction with the single-stranded DNA-binding protein gp32 and the recombination mediator UvsY modulates gp47 nuclease activity to couple DNA end resection directly to presynaptic filament assembly during double-strand break repair, homologous recombination, and recombination-dependent DNA replication, as well as exonucleolytic degradation of fragmented host chromosomal DNA into mononucleotides.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000043 | ACCEPT | Summary: gp47 directly binds double-stranded and single-stranded DNA substrates at its Mre11-like nuclease active site and allosterically activates gp46 ATPase activity in the presence of DNA. Reason: DNA binding is an essential aspect of gp47 substrate recognition and allosteric activation of the gp46/gp47 MR complex. Supporting Evidence: file:BPT4/47/47-deep-research-falcon.md Stimulation by Mre11 (gp47) + dsDNA: addition of both **Mre11 and DNA increases ATP hydrolysis ~20-fold**, with positive cooperativity (Hill coefficient increases from ~1.4 to ~2.4 in the MR-DNA condition). |
| GO:0004518 nuclease activity | IEA GO_REF:0000043 | MODIFY | Summary: gp47 is the catalytic metallophosphoesterase nuclease subunit of the T4 gp46/gp47 exonuclease complex. Reason: Nuclease activity (GO:0004518) is a broad parent term; exonuclease activity (GO:0004527) is already present and more specifically captures the primary DNA end-resection activity of gp47. Proposed replacements: exonuclease activity Supporting Evidence: file:BPT4/47/47-uniprot.txt FUNCTION: Exonuclease that plays a role in viral genome replication, DNA recombination, and host DNA degradation. file:BPT4/47/47-deep-research-falcon.md The target protein specified by UniProt accession **P04521** corresponds to **gene product 47 (gp47)** from **Enterobacteria phage T4** and is consistently identified in the literature as the **T4 Mre11 homolog** (nuclease subunit) that partners with **gp46 (Rad50 homolog)** to form the **Mre11–Rad50 (MR) complex**. |
| GO:0004527 exonuclease activity | IEA GO_REF:0000043 | ACCEPT | Summary: gp47 provides the calcineurin-like metallophosphoesterase active site that catalyzes ATP-stimulated double-stranded DNA exonuclease activity within the gp46/gp47 complex. Reason: Exonuclease activity (GO:0004527) directly represents the core catalytic function of gp47 in DNA end resection and host chromosome degradation. Supporting Evidence: file:BPT4/47/47-uniprot.txt FUNCTION: Exonuclease that plays a role in viral genome replication, DNA recombination, and host DNA degradation. file:BPT4/47/47-deep-research-falcon.md In T4, the **gp46/gp47 complex** is described as a major exonuclease activity for DSB resection in HR models of the T4 system (orthologous to eukaryotic Mre11/Rad50). |
| GO:0006281 DNA repair | IEA GO_REF:0000043 | MODIFY | Summary: gp47 is essential for recombinational repair of DNA double-strand breaks during T4 infection. Reason: DNA repair (GO:0006281) is overly general; gp47 specifically functions in double-strand break repair (GO:0006302) via nucleolytic resection of broken DNA ends. Proposed replacements: double-strand break repair Supporting Evidence: file:BPT4/47/47-deep-research-falcon.md 1. **Processing of DNA ends during DSB repair / HDR**, as part of the gp46/gp47 MR complex. |
| GO:0006974 DNA damage response | IEA GO_REF:0000043 | MODIFY | Summary: gp47 acts in the viral response to DNA damage by resecting double-strand breaks to initiate recombinational repair and replication restart. Reason: DNA damage response (GO:0006974) is a broad parent term; double-strand break repair (GO:0006302) more precisely captures the pathway role of gp47. Proposed replacements: double-strand break repair Supporting Evidence: file:BPT4/47/47-deep-research-falcon.md 1. **Processing of DNA ends during DSB repair / HDR**, as part of the gp46/gp47 MR complex. |
| GO:0016787 hydrolase activity | IEA GO_REF:0000120 | MODIFY | Summary: gp47 is a metallophosphoesterase hydrolase that cleaves phosphodiester bonds in DNA. Reason: Hydrolase activity (GO:0016787) is too general when exonuclease activity (GO:0004527) is already annotated and supported. Proposed replacements: exonuclease activity Supporting Evidence: file:BPT4/47/47-uniprot.txt FUNCTION: Exonuclease that plays a role in viral genome replication, DNA recombination, and host DNA degradation. |
| GO:0039657 symbiont-mediated suppression of host gene expression | IEA GO_REF:0000043 | MODIFY | Summary: gp47 is a subunit of the gp46/gp47 recombination nuclease complex that degrades cytosine-containing host chromosomal DNA; refine broad host gene expression suppression to degradation of host chromosome by virus. Reason: While immediate transcriptional shutoff of E. coli is initiated by Alc, AsiA, Alt, and ModA, the gp46/gp47 Mre11/Rad50-like nuclease complex degrades cytosine-containing host chromosomal DNA following Endonuclease II/IV cleavage, permanently eliminating the host template. The annotation is therefore best refined from GO:0039657 (symbiont-mediated suppression of host gene expression) to the specific mechanism GO:0099015 (degradation of host chromosome by virus). Proposed replacements: degradation of host chromosome by virus Supporting Evidence: file:BPT4/47/47-uniprot.txt FUNCTION: Exonuclease that plays a role in viral genome replication, DNA recombination, and host DNA degradation. |
| GO:0099015 degradation of host chromosome by virus | IEA GO_REF:0000043 | ACCEPT | Summary: Together with gp46, gp47 is required for the exonucleolytic breakdown of cytosine-containing Escherichia coli chromosomal DNA into acid-soluble mononucleotides for viral DNA synthesis. Reason: Genetic studies (Kutter & Wiberg 1968) demonstrated that gene 47 mutants accumulate partially cleaved host chromosomal DNA fragments and fail to degrade them into mononucleotides. Supporting Evidence: file:BPT4/47/47-uniprot.txt FUNCTION: Exonuclease that plays a role in viral genome replication, DNA recombination, and host DNA degradation. file:BPT4/47/47-deep-research-falcon.md 3. A proposed role in **host genomic DNA processing/degradation** to supply deoxynucleotides for phage DNA synthesis (noted as a physiological rationale for relatively rapid MR activities in T4 compared with other MR systems). |
Loading supporting content…
Download this section (compressed HTML)Q: How do gp32 and UvsY physically engage gp47 to switch its divalent cation selectivity from Mn2+-dependent 3'-5' exonucleolysis to Mg2+-dependent endonucleolytic cleavage near DNA ends?
Q: Does gp47 distinguish between hydroxymethylcytosine-glucosylated T4 DNA ends (destined for limited resection and recombinational repair) and nonglucosylated cytosine-containing host DNA fragments (destined for complete degradation)?
Experiment: Compare the cleavage kinetics and product profiles of reconstituted gp46/gp47-gp32-UvsY complexes on unmodified cytosine-containing dsDNA vs glucosyl-hydroxymethylcytosine T4 dsDNA substrates in physiological Mg2+ buffers.
Hypothesis: Glucosyl-hydroxymethylcytosine modifications and rapid UvsY/UvsX filament nucleation restrict gp47 resection on phage DNA ends after generating a 3' single-stranded tail, whereas unmodified host DNA fragments undergo extensive exonucleolytic digestion.
Experiment: Perform hydrogen-deuterium exchange mass spectrometry (HDX-MS) on gp47 in the gp46/gp47 complex upon addition of gp32 and UvsY.
Hypothesis: UvsY and gp32 bind a surface patch on gp47 adjacent to the capping domain, allosterically repositioning the catalytic His/Asp motifs to favor Mg2+-assisted endonucleolytic incision of the 5'-terminated strand.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)