| Functional aspect | Key result with quantitative numbers where available | Evidence type | System/assay | Citation (author year) | URL/DOI |
|---|---|---|---|---|---|
| Target identity / family | Dda from bacteriophage T4 is a monomeric SF1B helicase related to the Pif1 family; crystal structure solved with ssDNA (PDB 3UPU), matching the UniProt assignment for P32270 | Structural, biochemistry | X-ray crystallography of Dda–ssDNA complex; comparative helicase analysis (pqac-00000004, pqac-00000006, pqac-00000023) | He et al. 2012 | https://doi.org/10.1016/j.str.2012.04.013 |
| Directionality | Dda translocates/unwinds in the 5′→3′ direction on ssDNA | Bulk biochemistry | Helicase/translocation assays on tailed DNA substrates; streptavidin-block directionality tests (pqac-00000000, pqac-00000002, pqac-00000006, pqac-00000021) | Raney & Benkovic 1995; He et al. 2012 | https://doi.org/10.1074/jbc.270.38.22236; https://doi.org/10.1016/j.str.2012.04.013 |
| Unwinding rate | Average duplex unwinding rate ≈ 257 ± 42 bp/s under single-molecule/bulk analysis | Single-molecule, bulk biochemistry | DNA unwinding assays with optical/single-molecule and ensemble kinetics (pqac-00000000, pqac-00000005) | Byrd et al. 2012 | https://doi.org/10.1016/j.jmb.2012.04.007 |
| ssDNA translocation rate | Average ssDNA translocation rate ≈ 267 ± 15 nt/s; wild-type fitted ktrans ≈ 233 ± 27 nt/s in structural/kinetic study | Single-molecule, stopped-flow, bulk biochemistry | ssDNA translocation assays and kinetic modeling (pqac-00000000, pqac-00000003, pqac-00000005) | Byrd et al. 2012; He et al. 2012 | https://doi.org/10.1016/j.jmb.2012.04.007; https://doi.org/10.1016/j.str.2012.04.013 |
| Coupling efficiency / helicase mechanism | Vun/Vtrans ≈ 0.96, indicating Dda is an “optimally active” helicase with tight coupling of translocation to strand separation; unwinding is largely insensitive to GC content and applied force | Single-molecule, bulk biochemistry | Comparison of ssDNA translocation and dsDNA unwinding; force and duplex stability dependence (pqac-00000000, pqac-00000005) | Byrd et al. 2012 | https://doi.org/10.1016/j.jmb.2012.04.007 |
| Processivity / dissociation | Wild-type dissociation rate from ssDNA reported as kd ≈ 5.75 ± 1.60 s^-1; modeled ssDNA binding site ~8 nt; Dda is intrinsically low/moderate processivity, increased when multiple Dda molecules load | Bulk biochemistry, kinetics | Stopped-flow translocation kinetics; unwinding processivity analysis (pqac-00000003, pqac-00000008, pqac-00000013) | He et al. 2012; Jordan & Morrical 2015 | https://doi.org/10.1016/j.str.2012.04.013; https://doi.org/10.1016/j.dnarep.2014.10.002 |
| Structural strand-separation mechanism | The 1B “pin” with Phe98 is essential for duplex separation; F98A abolishes unwinding while preserving ssDNA translocation. The pin is braced by tower/SH3 architecture to couple ATP-driven motion to strand separation | Structural, mutational biochemistry | Dda–ssDNA crystal structure; mutant translocation/unwinding assays (pqac-00000003, pqac-00000024, pqac-00000025) | He et al. 2012 | https://doi.org/10.1016/j.str.2012.04.013 |
| Mutant quantitative example | F98A retains ssDNA translocation (ktrans ≈ 249 ± 23 nt/s) but shows increased dissociation (kd ≈ 20.4 ± 2.3 s^-1) and loss of unwinding, separating translocation from duplex-splitting function | Structural, kinetics | Site-directed mutagenesis plus stopped-flow/unwinding assays (pqac-00000003) | He et al. 2012 | https://doi.org/10.1016/j.str.2012.04.013 |
| Fork engagement / displaced-strand contacts | Dda unwinds fork DNA more processively than ss/ds junction substrates; fork binding disrupts ~2 bp before unwinding, supporting simultaneous contacts with tracking strand, displaced strand, and duplex | Bulk biochemistry | DNA footprinting and kinetic unwinding on fork versus junction substrates (pqac-00000015) | Aarattuthodiyil et al. 2014 | https://doi.org/10.1093/nar/gku845 |
| gp32 regulation | gp32 is an essential cofactor for Dda-stimulated strand-displacement synthesis; direct gp32–Dda protein–protein interactions are required, and Dda binds tightly to gp32 even without ssDNA | Bulk biochemistry | Reconstituted T4 fork DNA synthesis with gp32 variants and Dda (pqac-00000008, pqac-00000012, pqac-00000015, pqac-00000020) | Ma et al. 2004; Jordan & Morrical 2015 | https://doi.org/10.1074/jbc.m311738200; https://doi.org/10.1016/j.dnarep.2014.10.002 |
| Dual effect of gp32 | gp32–Dda interactions can stimulate Dda unwinding and ATP turnover, especially at higher salt and in the presence of DNA polymerase, but gp32 clusters on ssDNA can also sterically inhibit Dda loading/unwinding depending on geometry | Bulk biochemistry, mechanistic model | Unwinding and ATPase analyses with gp32, gp32 fragments, and fork substrates (pqac-00000008, pqac-00000013, pqac-00000020, pqac-00000022) | Jordan & Morrical 2015 | https://doi.org/10.1016/j.dnarep.2014.10.002 |
| gp32 interaction surface | The acidic C-terminal A-domain of gp32 mediates protein–protein interactions with Dda; gp32 fragments lacking this domain lose interaction despite near-normal ssDNA binding | Bulk biochemistry | gp32 truncation/mutant analysis in helicase-loading and strand-displacement reactions (pqac-00000015) | Ma et al. 2004 | https://doi.org/10.1074/jbc.m311738200 |
| UvsX / branch migration | Dda binds UvsX and stimulates UvsX-catalyzed branch migration about 4-fold in vitro, linking Dda to recombination-dependent DNA metabolism | Bulk biochemistry | Protein interaction and branch-migration assays (pqac-00000009, pqac-00000011, pqac-00000021) | Hacker & Alberts 1992; Gauss et al. 1994 | https://doi.org/10.1016/S0021-9258(19)36738-9; https://doi.org/10.1128/jb.176.6.1667-1672.1994 |
| Replication-fork rescue / lesion bypass | UvsX plus Dda are sufficient to rescue stalled T4 replication forks in vitro through sequential template-switching reactions that bypass a non-coding lesion without mutagenesis | Bulk biochemistry | Reconstituted stalled T4 fork rescue assay (pqac-00000008) | Kadyrov & Drake 2004 | https://doi.org/10.1074/jbc.m403942200 |
| Origin-dependent replication role | dda mutants show delayed early DNA synthesis, indicating a role in origin-dependent initiation; Dda is nonessential alone but strongly synergizes genetically with gp59 defects | Genetics/in vivo | T4 infection time-course and mutant analysis (pqac-00000004, pqac-00000009, pqac-00000014, pqac-00000021) | Gauss et al. 1994; Brister 2008 | https://doi.org/10.1128/jb.176.6.1667-1672.1994; https://doi.org/10.1016/j.jmb.2008.02.002 |
| Origin activation genome-wide | In dda mutants, synthesis no longer preferentially initiates near origins; model proposes Dda unwinds origin DNA, clears bound proteins, and creates a ssDNA landing zone for gp41 loading | Genetics/in vivo | Genome-wide replication/origin activation analysis during infection (pqac-00000014) | Brister 2008 | https://doi.org/10.1016/j.jmb.2008.02.002 |
| Genetic interaction with gp59 | Combined dda and gp59 defects cause essentially no DNA synthesis, indicating overlapping/synergistic roles in establishing productive replication forks | Genetics/in vivo | Double-mutant infection analysis (pqac-00000004, pqac-00000009, pqac-00000021) | Gauss et al. 1994; He et al. 2012 | https://doi.org/10.1128/jb.176.6.1667-1672.1994; https://doi.org/10.1016/j.str.2012.04.013 |
| Protein displacement activity | Dda can displace proteins from DNA, including streptavidin and trp repressor; multiple Dda molecules enhance displacement efficiency when obstacles are present | Bulk biochemistry, single-molecule context | Protein–DNA displacement assays on biotinylated or protein-bound DNA substrates (pqac-00000000, pqac-00000005, pqac-00000019) | Byrd et al. 2012; Byrd et al. 2022 | https://doi.org/10.1016/j.jmb.2012.04.007; https://doi.org/10.1002/pro.4232 |
| Structural determinant of protein displacement | A SH3-domain “hook” subdomain (Δ279–284 deletion) leaves DNA binding and maximal ATPase largely intact but markedly reduces streptavidin displacement and lowers unwinding processivity, showing separable determinants for unwinding versus protein eviction | Structural, mutational biochemistry | Domain deletion and protein-displacement assays (pqac-00000019) | Byrd et al. 2022 | https://doi.org/10.1002/pro.4232 |
| Functional localization | Dda acts on phage DNA replication and recombination intermediates in the infected bacterial cytoplasm/nucleoid context, especially at replication forks, origins, and recombination-generated branched DNA rather than as a virion structural protein | Inference from genetics/biochemistry | Infected-cell replication phenotypes plus in vitro fork/origin/recombination substrates (pqac-00000004, pqac-00000008, pqac-00000014) | He et al. 2012; Jordan & Morrical 2015; Brister 2008 | https://doi.org/10.1016/j.str.2012.04.013; https://doi.org/10.1016/j.dnarep.2014.10.002; https://doi.org/10.1016/j.jmb.2008.02.002 |


*Table: This table summarizes experimentally supported findings for bacteriophage T4 Dda helicase (UniProt P32270), covering mechanism, kinetics, partner interactions, and biological roles in replication and recombination. It is useful as a compact evidence map linking each claim to assay type and source.*