DNA helicase gp41 is a 475-amino-acid superfamily 4 (DnaB-like) hexameric replicative DNA helicase that serves as the primary fork-unwinding motor of the bacteriophage T4 replisome. Upon binding ATP or GTP, gp41 assembles into a ring-shaped homohexamer that is loaded onto gp32-coated replication forks and recombination intermediates by the helicase loader gp59. Translocating in the 5' to 3' direction along the lagging-strand template, gp41 unwinds duplex DNA ahead of the leading-strand gp43 DNA polymerase and associates directly with the gp61 primase to form the primosome, coordinating lagging-strand RNA primer synthesis with rapid replication fork progression during origin-dependent and recombination-dependent viral DNA replication.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000166 nucleotide binding | IEA GO_REF:0000043 | MODIFY | Summary: gp41 binds nucleoside triphosphates (primarily ATP and GTP) to promote hexamerization and fuel DNA unwinding. Reason: Nucleotide binding (GO:0000166) is overly broad; ATP binding (GO:0005524) is already annotated and more specifically captures the primary physiological nucleotide ligand of gp41. Proposed replacements: ATP binding Supporting Evidence: PMID:8107085 The bacteriophage T4 gene 41 helicase protein (gp41) carries a single-stranded DNA-dependent ATPase activity that is essential to its helicase activity. |
| GO:0003677 DNA binding | IEA GO_REF:0000043 | ACCEPT | Summary: gp41 binds single-stranded and forked DNA substrates, encircling the lagging-strand template within its hexameric central channel. Reason: Direct DNA binding is experimentally demonstrated and essential for gp41 translocation and duplex unwinding. Supporting Evidence: PMID:10871615 Consistent with the roles of these proteins in recombination, we find that 59 protein binds to and stimulates 41 helicase activity on Holliday junction DNA, and on a substrate that resembles a strand invasion structure. PMID:8107085 The bacteriophage T4 gene 41 helicase protein (gp41) carries a single-stranded DNA-dependent ATPase activity that is essential to its helicase activity. |
| GO:0003678 DNA helicase activity | IEA GO_REF:0000120 | ACCEPT | Summary: gp41 catalyzes ATP-dependent 5'-3' unwinding of duplex DNA at replication forks and recombination intermediates. Reason: DNA helicase activity (GO:0003678) is the core molecular function of gp41. Supporting Evidence: file:BPT4/41/41-uniprot.txt ATP-dependent DNA helicase essential for viral DNA replication and recombination (PubMed:10871615). PMID:10871615 Consistent with the roles of these proteins in recombination, we find that 59 protein binds to and stimulates 41 helicase activity on Holliday junction DNA, and on a substrate that resembles a strand invasion structure. |
| GO:0004386 helicase activity | IEA GO_REF:0000043 | MODIFY | Summary: gp41 is specifically a DNA helicase that unwinds double-stranded DNA. Reason: Helicase activity (GO:0004386) is too general when DNA helicase activity (GO:0003678) is directly supported and already present in the annotations. Proposed replacements: DNA helicase activity Supporting Evidence: file:BPT4/41/41-uniprot.txt ATP-dependent DNA helicase essential for viral DNA replication and recombination (PubMed:10871615). |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: gp41 binds ATP to drive hexamer assembly and power ssDNA translocation and duplex DNA unwinding. Reason: ATP binding (GO:0005524) is well established for gp41 oligomerization and catalytic turnover. Supporting Evidence: PMID:8107085 The bacteriophage T4 gene 41 helicase protein (gp41) carries a single-stranded DNA-dependent ATPase activity that is essential to its helicase activity. file:BPT4/41/41-deep-research-falcon.md **gp41 is the T4 replicative helicase** and functions as an **ssDNA-stimulated ATPase/GTPase** whose NTP hydrolysis drives **5′→3′ translocation** on ssDNA and **fork unwinding**. |
| GO:0006260 DNA replication | IEA GO_REF:0000120 | MODIFY | Summary: gp41 is the essential replicative helicase for T4 viral DNA replication. Reason: DNA replication (GO:0006260) is a general parent term; bidirectional double-stranded viral DNA replication (GO:0039686) is already annotated with experimental evidence and more specifically describes this biological process. Proposed replacements: bidirectional double-stranded viral DNA replication Supporting Evidence: PMID:15781450 We also found that all origin-replicative intermediates were absent in infections deficient in the helicase gp41 or the single-strand-binding protein gp32, regardless of whether gp59 was present or absent. |
| GO:0006269 DNA replication, synthesis of primer | IEA GO_REF:0000043 | KEEP AS NON CORE | Summary: gp41 forms the primosome complex with the gp61 primase and is required to recruit and stimulate gp61 for lagging-strand RNA primer synthesis. Reason: While gp61 catalyzes the actual synthesis of the pentaribonucleotide primer, gp41 forms the obligate primosome complex with gp61 and allosterically stimulates primer synthesis during lagging-strand replication. Supporting Evidence: file:BPT4/41/41-uniprot.txt Interaction with the primase allows the primase to initiate lagging strand synthesis and fully activates the helicase (PubMed:22869700, PubMed:23578280). |
| GO:0016787 hydrolase activity | IEA GO_REF:0000043 | MODIFY | Summary: gp41 hydrolyzes nucleoside triphosphates to catalyze DNA duplex unwinding. Reason: Hydrolase activity (GO:0016787) is an uninformative high-level term; DNA helicase activity (GO:0003678) is a specific descendant that captures the enzymatic function of gp41. Proposed replacements: DNA helicase activity Supporting Evidence: file:BPT4/41/41-uniprot.txt ATP-dependent DNA helicase essential for viral DNA replication and recombination (PubMed:10871615). |
| GO:0039686 bidirectional double-stranded viral DNA replication | IEA GO_REF:0000002 | ACCEPT | Summary: gp41 is the replicative helicase required for origin-initiated and recombination-dependent double-stranded viral DNA replication in T4. Reason: Reinforces the experimental annotation (PMID:15781450) showing that gp41 is essential for viral dsDNA replication. Supporting Evidence: PMID:15781450 We also found that all origin-replicative intermediates were absent in infections deficient in the helicase gp41 or the single-strand-binding protein gp32, regardless of whether gp59 was present or absent. |
| GO:0039693 viral DNA genome replication | IEA GO_REF:0000043 | MODIFY | Summary: gp41 unwinds the viral dsDNA genome during replication fork progression. Reason: Viral DNA genome replication (GO:0039693) is broader than its child term bidirectional double-stranded viral DNA replication (GO:0039686), which is already present with experimental support. Proposed replacements: bidirectional double-stranded viral DNA replication Supporting Evidence: PMID:15781450 We also found that all origin-replicative intermediates were absent in infections deficient in the helicase gp41 or the single-strand-binding protein gp32, regardless of whether gp59 was present or absent. |
| GO:0003678 DNA helicase activity | IDA PMID:10871615 Interaction of the bacteriophage T4 gene 59 helicase loading... | ACCEPT | Summary: Purified gp41 unwinds forked DNA, Holliday junctions, and strand invasion structures in an ATP-dependent manner that is stimulated by gp59. Reason: Direct biochemical assays in PMID:10871615 demonstrate DNA helicase activity of gp41 on branched replication and recombination substrates. Supporting Evidence: PMID:10871615 Consistent with the roles of these proteins in recombination, we find that 59 protein binds to and stimulates 41 helicase activity on Holliday junction DNA, and on a substrate that resembles a strand invasion structure. |
| GO:0017116 single-stranded DNA helicase activity | IDA PMID:8107085 Kinetic parameters of the translocation of bacteriophage T4 ... | ACCEPT | Summary: gp41 translocates processively along single-stranded DNA in a 5'-3' direction coupled to ATP hydrolysis to unwind duplex DNA. Reason: PMID:8107085 directly characterizes the ssDNA-dependent ATPase translocation and helicase unwinding mechanism of gp41. Supporting Evidence: PMID:8107085 The bacteriophage T4 gene 41 helicase protein (gp41) carries a single-stranded DNA-dependent ATPase activity that is essential to its helicase activity. |
| GO:0039686 bidirectional double-stranded viral DNA replication | IDA PMID:15781450 Bacteriophage T4 helicase loader protein gp59 functions as g... | ACCEPT | Summary: Two-dimensional gel electrophoresis of T4 replication intermediates in vivo demonstrates that gp41 is essential for origin-dependent double-stranded viral DNA replication. Reason: Direct in vivo evidence in PMID:15781450 confirms that gp41 is indispensable for origin-replicative intermediates during T4 dsDNA replication. Supporting Evidence: PMID:15781450 We also found that all origin-replicative intermediates were absent in infections deficient in the helicase gp41 or the single-strand-binding protein gp32, regardless of whether gp59 was present or absent. |
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Download this section (compressed HTML)Q: What is the high-resolution structural mechanism by which the gp59 helicase loader opens the hexameric gp41 ring to thread the lagging-strand template into the central channel?
Q: How does transient physical coupling between the moving gp41 hexamer and the leading-strand gp43 DNA polymerase switch gp41 from a passive ~30 bp/s unwinding mode to rapid (~400 bp/s) replisomal unwinding?
Experiment: Resolve cryo-EM structures of the T4 primosome-loading intermediate containing forked DNA, gp32, gp59, gp41, and gp61 in the presence of ADP-BeFx.
Hypothesis: gp59 wedges into a single subunit interface of the gp41 hexamer, stabilizing a cracked right-handed spiral conformation that closes into a planar translocating ring upon gp61 binding and ATP hydrolysis.
Experiment: Perform single-molecule magnetic tweezers unwinding assays with gp41 and gp43 variants carrying targeted mutations in their C-terminal and N-terminal surface loops.
Hypothesis: A flexible electrostatic tether between the C-terminal tail of gp41 and the palm/thumb domain of gp43 prevents polymerase-helicase uncoupling and DNA rezipping behind the advancing helicase.
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