ATP-dependent DNA helicase Dda (DNA-dependent ATPase) is a 439-amino-acid superfamily 1B (SF1B) 5'-3' DNA helicase of bacteriophage T4. Capable of unwinding duplex DNA at rates of ~250 bp/s as a monomer and generating higher displacement forces when multiple monomers assemble along single-stranded DNA, Dda couples ssDNA-stimulated ATP hydrolysis to 5'-3' translocation, duplex unwinding, and displacement of DNA-bound protein roadblocks such as host RNA polymerase. In vivo and in vitro, Dda facilitates early origin-dependent viral DNA replication initiation, clears protein barriers ahead of the replication fork, and cooperates with UvsX and gp32 in recombinational template switching.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000166 nucleotide binding | IEA GO_REF:0000043 | MODIFY | Summary: Dda binds ATP at its superfamily 1B RecA-like motor core to power DNA translocation and unwinding. Reason: Nucleotide binding (GO:0000166) is overly general; ATP binding (GO:0005524) is already present and specifically identifies the physiological nucleotide substrate. Proposed replacements: ATP binding Supporting Evidence: file:BPT4/dda/dda-deep-research-falcon.md Dda is a helicase that uses **ATP hydrolysis** to move along **single-stranded DNA (ssDNA)** and unwind **double-stranded DNA (dsDNA)** junctions encountered during translocation. |
| GO:0004386 helicase activity | IEA GO_REF:0000043 | MODIFY | Summary: Dda is an ATP-dependent DNA helicase that unwinds duplex DNA in the 5' to 3' direction. Reason: Helicase activity (GO:0004386) is too general when the more specific descendant 5'-3' DNA helicase activity (GO:0043139) is experimentally established and already annotated on this gene. Proposed replacements: 5'-3' DNA helicase activity Supporting Evidence: PMID:1328208 The bacteriophage T4 dda protein is a 5'-3' DNA helicase that stimulates DNA replication and recombination reactions in vitro and seems to play a role in the initiation of T4 DNA replication in vivo. |
| GO:0005524 ATP binding | IEA GO_REF:0000043 | ACCEPT | Summary: Dda binds ATP at its conserved Walker A/B P-loop motifs to drive its helicase motor cycle. Reason: ATP binding is essential for the DNA-dependent ATPase and 5'-3' helicase activities of Dda. Supporting Evidence: file:BPT4/dda/dda-deep-research-falcon.md Dda is a helicase that uses **ATP hydrolysis** to move along **single-stranded DNA (ssDNA)** and unwind **double-stranded DNA (dsDNA)** junctions encountered during translocation. |
| GO:0006260 DNA replication | IEA GO_REF:0000043 | ACCEPT | Summary: Dda stimulates early origin-dependent T4 DNA replication initiation, promotes fork progression past protein roadblocks, and supports template-switching DNA synthesis. Reason: Genetic and biochemical studies demonstrate that Dda participates in viral DNA replication initiation and replication past DNA-bound RNA polymerase barriers. Supporting Evidence: PMID:1328208 The bacteriophage T4 dda protein is a 5'-3' DNA helicase that stimulates DNA replication and recombination reactions in vitro and seems to play a role in the initiation of T4 DNA replication in vivo. PMID:7806534 A second, very different DNA helicase, the T4 dda protein, provides an alternative pathway for replication past this DNA-bound RNA polymerase |
| GO:0016787 hydrolase activity | IEA GO_REF:0000043 | MODIFY | Summary: Dda catalyzes ssDNA-dependent ATP hydrolysis to drive 5'-3' DNA unwinding. Reason: Hydrolase activity (GO:0016787) is overly general; the specific descendant terms 5'-3' DNA helicase activity (GO:0043139) and ATP hydrolysis activity (GO:0016887) are already annotated and experimentally supported. Proposed replacements: 5'-3' DNA helicase activity ATP hydrolysis activity Supporting Evidence: PMID:1328208 The bacteriophage T4 dda protein is a 5'-3' DNA helicase that stimulates DNA replication and recombination reactions in vitro and seems to play a role in the initiation of T4 DNA replication in vivo. |
| GO:0016853 isomerase activity | IEA GO_REF:0000043 | MODIFY | Summary: Dda is an ATP-dependent 5'-3' DNA helicase classified under EC 5.6.2.3; refine broad isomerase mapping to 5'-3' DNA helicase activity. Reason: DNA helicases (EC 5.6.2.-) were reclassified by IUBMB into EC class 5 (isomerases, UniProt keyword KW-0413), which generates the broad GO:0016853 isomerase activity IEA mapping. Because Dda specifically catalyzes ATP-dependent 5'-3' DNA duplex unwinding (EC 5.6.2.3), this broad mapping should be refined to GO:0043139 (5'-3' DNA helicase activity). Proposed replacements: 5'-3' DNA helicase activity Supporting Evidence: file:BPT4/dda/dda-uniprot.txt Unwinds DNA as a monomer in a 5'-3' direction at a rate of 250 bp/s and can efficiently displace proteins from the DNA (PubMed:17823128, PubMed:22504228). PMID:1328208 The bacteriophage T4 dda protein is a 5'-3' DNA helicase that stimulates DNA replication and recombination reactions in vitro and seems to play a role in the initiation of T4 DNA replication in vivo. |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000116 | ACCEPT | Summary: Dda hydrolyzes ATP in a single-stranded DNA-dependent manner to power unidirectional 5'-3' translocation and duplex unwinding. Reason: ATP hydrolysis activity (GO:0016887) is an intrinsic catalytic activity of Dda, supported by both Rhea mapping and experimental characterization. Supporting Evidence: file:BPT4/dda/dda-deep-research-falcon.md Dda is a helicase that uses **ATP hydrolysis** to move along **single-stranded DNA (ssDNA)** and unwind **double-stranded DNA (dsDNA)** junctions encountered during translocation. |
| GO:0043139 5'-3' DNA helicase activity | IEA GO_REF:0000003 | ACCEPT | Summary: Dda unwinds duplex DNA specifically in the 5' to 3' direction along single-stranded DNA. Reason: Reinforces the experimental annotations (PMID:12411580, PMID:17823128) for 5'-3' DNA helicase activity. Supporting Evidence: file:BPT4/dda/dda-uniprot.txt Unwinds DNA as a monomer in a 5'-3' direction at a rate of 250 bp/s and can efficiently displace proteins from the DNA (PubMed:17823128, PubMed:22504228). |
| GO:0016887 ATP hydrolysis activity | EXP PMID:1328208 Overexpression, purification, sequence analysis, and charact... | ACCEPT | Summary: Purified recombinant Dda exhibits potent DNA-dependent ATPase activity that drives its 5'-3' DNA helicase function. Reason: PMID:1328208 purified and biochemically characterized Dda as a DNA-dependent ATPase and 5'-3' helicase. Supporting Evidence: PMID:1328208 The bacteriophage T4 dda protein is a 5'-3' DNA helicase that stimulates DNA replication and recombination reactions in vitro and seems to play a role in the initiation of T4 DNA replication in vivo. |
| GO:0043139 5'-3' DNA helicase activity | EXP PMID:12411580 Pre-steady-state DNA unwinding by bacteriophage T4 Dda helic... | ACCEPT | Summary: Pre-steady-state rapid-quench unwinding assays demonstrate that monomeric Dda rapidly unwinds duplex DNA overhangs with 5'-3' polarity. Reason: Direct pre-steady-state kinetic evidence in PMID:12411580 establishes 5'-3' DNA helicase activity of monomeric Dda. Supporting Evidence: PMID:12411580 Thus, Dda can rapidly unwind oligonucleotide substrates as a monomer, indicating that the functional molecular motor component of a helicase can reside within a single polypeptide. |
| GO:0043139 5'-3' DNA helicase activity | EXP PMID:17823128 The phage T4 protein UvsW drives Holliday junction branch mi... | ACCEPT | Summary: Dda acts as a 5'-3' DNA helicase that cooperates with UvsX to promote template switching by T4 DNA polymerase, distinct from Holliday junction branch migration by UvsW. Reason: PMID:17823128 directly assays Dda 5'-3' helicase activity in reconstituted recombinational repair and strand-switching reactions. Supporting Evidence: PMID:17823128 In this system, the strand exchange protein UvsX and the Dda helicase promoted strand switching by T4 polymerase. |
| GO:0004386 helicase activity | IDA PMID:7806534 A role for two DNA helicases in the replication of T4 bacter... | MODIFY | Summary: Dda helicase enables the T4 replication apparatus to replicate past DNA-bound Escherichia coli RNA polymerase complexes. Reason: While PMID:7806534 provides direct evidence of Dda helicase function, the more specific term 5'-3' DNA helicase activity (GO:0043139) is already annotated on this gene and should be used consistently across all rows for helicase activity. Proposed replacements: 5'-3' DNA helicase activity Supporting Evidence: PMID:7806534 A second, very different DNA helicase, the T4 dda protein, provides an alternative pathway for replication past this DNA-bound RNA polymerase |
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Download this section (compressed HTML)Q: How does the SH3-like tower/pin domain of Dda sense and destabilize high-affinity protein-DNA roadblocks such as stalled Escherichia coli RNA polymerase without forming a stable ring around the template strand?
Q: What governs the handoff at T4 replication origins between early Dda-mediated duplex opening and gp59-dependent loading of the hexameric gp41 replicative helicase?
Experiment: Use correlative optical tweezers and single-molecule fluorescence microscopy to visualize fluorescently labeled Dda monomers colliding with stalled E. coli RNA polymerase elongation complexes on stretched phage DNA templates.
Hypothesis: Trailing Dda monomers pile up behind a leading monomer at the RNA polymerase barrier, preventing backward slippage and rectifying thermal fluctuations of the transcription bubble until RNA polymerase dissociates.
Experiment: Reconstitute T4 origin R-loop unwinding in vitro with purified RNase H, gp32, Dda, gp59, and gp41 to measure the effect of Dda on the kinetics of gp41 hexamer loading.
Hypothesis: Monomeric Dda rapidly expands the initial origin ssDNA bubble to expose a gp32-coated lagging-strand loading site required for gp59-mediated gp41 recruitment.
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