| Category | Finding (with numeric values) | Experimental context/assay | Key reference (author year) | DOI/URL | Publication date |
|---|---|---|---|---|---|
| Enzymatic activity | gp41 is a DNA-dependent ATPase/GTPase and replicative helicase; ssDNA strongly stimulates NTPase activity; ATP hydrolysis drives unwinding at ~1 bp per ATP hydrolyzed | Biochemical helicase/NTPase assays; structural review synthesis (pqac-00000017, pqac-00000018) | Nelson et al. 2009; Mueser et al. 2010 | https://doi.org/10.1007/b135974_16 ; https://doi.org/10.1186/1743-422x-7-359 | Jan 2009; Dec 2010 |
| Directionality | Translocates 5′→3′ on ssDNA, encircling the lagging strand and excluding the leading strand at the fork (pqac-00000018, pqac-00000020) | Fork-substrate biochemical assays; replisome reviews | Mueser et al. 2010; Noble et al. 2015 | https://doi.org/10.1186/1743-422x-7-359 ; https://doi.org/10.3390/v7062766 | Dec 2010; Jun 2015 |
| Substrate requirements | Preferred substrate is forked DNA; absolute requirement for a 5′ ssDNA tail ≥32 nt; optimal unwinding also requires a 3′ ssDNA extension >29 nt; gp59 reduces these tail-length requirements (pqac-00000017, pqac-00000032) | Forked-DNA unwinding and loading assays summarized from primary studies | Nelson et al. 2009 | https://doi.org/10.1007/b135974_16 | Jan 2009 |
| DNA-binding footprint | Binding-site size estimated at 12–20 nt per gp41 monomer on ssDNA (pqac-00000017, pqac-00000032) | EMSA/oligonucleotide binding assays | Nelson et al. 2009 | https://doi.org/10.1007/b135974_16 | Jan 2009 |
| Oligomeric state | In solution gp41 exists in a monomer/dimer equilibrium (primarily dimer at physiological concentrations); ATP or ATPγS binding promotes assembly through dimers→tetramers→hexamers to form the active helicase (pqac-00000017, pqac-00000032) | Sedimentation/EM/cross-linking/biophysical studies summarized in review | Nelson et al. 2009 | https://doi.org/10.1007/b135974_16 | Jan 2009 |
| Conformations | Hexamers are toroidal rings; EM identified distinct “open/gapped” and “closed” conformations, with the open form proposed to facilitate loading onto DNA (pqac-00000016, pqac-00000032, pqac-00000034) | Electron microscopy and mechanistic review | Noble et al. 2015; Nelson et al. 2009 | https://doi.org/10.3390/v7062766 ; https://doi.org/10.1007/b135974_16 | Jun 2015; Jan 2009 |
| gp61 primase interaction | Functional primosome contains 6 gp41 subunits + 1 gp61 primase (6:1); gp41 stimulates gp61 RNA primer synthesis and shifts products toward pentaribonucleotides from 5′-GTT-3′ sites (pqac-00000007, pqac-00000031) | Reconstituted primosome, ATPase stimulation, footprinting, protein–DNA interaction mapping | Jing et al. 1999 | https://doi.org/10.1074/jbc.274.38.27287 | Sep 17 1999 |
| gp59 loader interaction | gp59 is the helicase loader; maximal enhancement of gp41 loading/unwinding at ~1:1 gp59:gp41 stoichiometry; gp59 can induce gp41 oligomerization and relax fork-tail requirements (pqac-00000019, pqac-00000028, pqac-00000036) | Loading/unwinding assays, cross-linking, fork-DNA assembly studies | Xi et al. 2005; Nelson et al. 2009 | https://doi.org/10.1021/bi047296w ; https://doi.org/10.1007/b135974_16 | May 2005; Jan 2009 |
| gp32 SSB interaction context | gp32 coats exposed ssDNA, prevents secondary structure, and supports helicase loading indirectly through gp59; gp59-gp32 interactions help place gp41 onto gp32-covered ssDNA/recombination intermediates (pqac-00000020, pqac-00000024, pqac-00000029) | Replisome assembly and recombination-dependent replication models | Noble et al. 2015; Nelson et al. 2009; Mueser et al. 2010 | https://doi.org/10.3390/v7062766 ; https://doi.org/10.1007/b135974_16 ; https://doi.org/10.1186/1743-422x-7-359 | Jun 2015; Jan 2009; Dec 2010 |
| gp43 polymerase coupling | gp41 and gp43 are functionally coupled at the fork, but no strong evidence for direct physical interaction in the absence of DNA; DNA-mediated coupling enables efficient strand-displacement synthesis (pqac-00000006, pqac-00000026) | Analytical ultracentrifugation and strand-displacement synthesis assays | Delagoutte & von Hippel 2001; Noble et al. 2015 | https://doi.org/10.1021/bi001306l ; https://doi.org/10.3390/v7062766 | Mar 2001; Jun 2015 |
| ssDNA translocation rate | ~400 nt/s; association half-life on ssDNA ~1 min (pqac-00000017, pqac-00000032) | gp41 translocation assays on ssDNA | Nelson et al. 2009 | https://doi.org/10.1007/b135974_16 | Jan 2009 |
| DNA unwinding rate | ~30 bp/s in the presence of gp59 (pqac-00000017) | Fork/unwinding assays with loader | Nelson et al. 2009 | https://doi.org/10.1007/b135974_16 | Jan 2009 |
| Coupled leading-strand unwinding/synthesis | ~250 bp/s (or nts/s in strand-displacement assays) when gp41 is coupled to a processive polymerase/holoenzyme; minimal gp41-gp43 complex can support ~90 nts/s under PEG-assisted loading conditions (pqac-00000023, pqac-00000017) | Strand-displacement DNA synthesis and helicase–polymerase coupling assays | Delagoutte & von Hippel 2001; Nelson et al. 2009 | https://doi.org/10.1021/bi001306l ; https://doi.org/10.1007/b135974_16 | Mar 2001; Jan 2009 |
| Processivity | Unwinding processivity on long duplex DNA is ~650 nt in the presence of gp61 primase (pqac-00000017) | Long-duplex unwinding with primase | Nelson et al. 2009 | https://doi.org/10.1007/b135974_16 | Jan 2009 |
| Replisome residence | Dissociation half-life of gp41 in the complete replisome is ~11 min, consistent with enough processivity to finish the 168 kb T4 genome at observed fork rates (pqac-00000017, pqac-00000032) | Dilution experiments in moving replisomes | Nelson et al. 2009 | https://doi.org/10.1007/b135974_16 | Jan 2009 |
| In vivo role/essentiality | Mutations in gene 41 strongly reduce T4 DNA replication and abolish lagging-strand synthesis; gp41 is therefore a core, essential replisome helicase during infection (pqac-00000017, pqac-00000032, pqac-00000033) | Genetic phenotypes summarized in replisome reviews | Nelson et al. 2009; Lee et al. 2013 | https://doi.org/10.1007/b135974_16 ; https://doi.org/10.1021/bi400231s | Jan 2009; May 2013 |
| Localization/function site | Functional localization is at the T4 DNA replication fork/primosome in the infected host cytoplasm; direct cell-imaging localization was not retrieved, so assignment is based on fork-specific biochemistry and replisome assembly data (pqac-00000034, pqac-00000035, pqac-00000039) | Replisome/primosome biochemical and structural models | Noble et al. 2015; Mueser et al. 2010; Jing et al. 1999 | https://doi.org/10.3390/v7062766 ; https://doi.org/10.1186/1743-422x-7-359 ; https://doi.org/10.1074/jbc.274.38.27287 | Jun 2015; Dec 2010; Sep 17 1999 |
| Recent structural advance (2023) | Cryo-EM captured gp41 alone as a right-handed open spiral and, after ssDNA binding, as a planar closed ring; conformational switch is “scissor-like” and activates helicase while exposing a hydrophobic surface for gp61 recruitment (pqac-00000040) | Stepwise in vitro reconstitution of T4 primosome; cryo-EM of helicase ± ssDNA ± primase | Feng et al. 2023 | https://doi.org/10.1038/s41467-023-40106-2 | Jul 2023 |
| Recent structural resolutions (2023) | Multiple T4 primosome cryo-EM maps were reported at ~5.7 Å to ~2.9–3.4 Å, defining gp41 activation and the bipartite binding mode of one gp61 primase per gp41 hexamer (pqac-00000040) | Cryo-EM structural series of assembly/function states | Feng et al. 2023 | https://doi.org/10.1038/s41467-023-40106-2 | Jul 2023 |
| 2024 broader relevance | 2024 reviews emphasize that modern cryo-EM, single-molecule methods, and AI structure prediction are reshaping understanding of bacterial/viral replicative helicases, providing context for functional annotation of DnaB-like systems such as T4 gp41 (pqac-00000042, pqac-00000043) | Review and AI-based structural modeling context | Shin et al. 2024 | https://doi.org/10.1128/jvi.01119-24 | Oct 2024 |


*Table: This table summarizes the main experimentally supported functional annotation facts for bacteriophage T4 gene product 41 (gp41), including activity, substrates, interactions, kinetics, and recent structural advances. It is useful as a compact evidence map for assigning molecular function, biological process, and localization.*