TraD is the type IV coupling protein of the F plasmid, a 717-residue inner membrane protein that connects the relaxosome to the secretion apparatus during conjugative DNA transfer. It is defined by what it joins rather than by a reaction it performs on its own: the relaxosome processes plasmid DNA at the origin of transfer, and TraD delivers that nucleoprotein complex to the membrane-spanning machine that translocates it into the recipient cell. The protein assembles into a hexameric ring that forms the cytoplasmic face of the conjugative pore, and it contacts the relaxosome through its C-terminal tail, which binds the relaxosome component TraM in grooves on a TraM tetramer. That tail is also the specificity determinant: shortening it lets TraD serve a broader range of mobilizable plasmids while reducing transfer of F itself. It belongs to the coupling-protein family whose other members include TrwB of R388, TraG of RP4 and VirD4 of the Agrobacterium T-DNA system.
The preferred accession for this review is P09130. These relationships are manually assessed.
Reviewed 2026-10-19 · Searched: UP000000625
Retain P09130 as the primary Swiss-Prot accession. No significant reference-proteome hit was returned. The reviewed entry explicitly derives from F and related plasmids, whereas the selected reference proteome does not provide a supported counterpart in this search. This is compatible with accessory-plasmid content; it is not proof of absence from E. coli K12 generally.
MMseqs2 searched 4,403 sequences across UP000000625 at E <= 1e-5 and sensitivity 7.5, returning 0 hits. The search table and candidate FASTA are empty; no alignments were generated. The heuristic search does not establish genomic absence or unique locus identity.
file:ECOLI/traD/traD-record-evidence.yaml
target_sequence_count: 4403
file:ECOLI/traD/traD-record-evidence.yaml
candidate_count: 0
The primary accession is outside every searched exact-taxon reference proteome.
file:ECOLI/traD/traD-record-evidence.yaml
primary_in_any_reference_proteome: false
Sampled UniSave observations: 11-NOV-2015, entry version 110.: no Proteomes cross-reference; 02-DEC-2020, entry version 128.: no Proteomes cross-reference; 27-NOV-2024, entry version 141.: no Proteomes cross-reference. These dated observations do not establish uninterrupted membership/absence, the exact change date, or UniProt's motivation.
file:ECOLI/traD/traD-record-evidence.yaml
entry_date: 11-NOV-2015, entry version 110. proteomes: []
file:ECOLI/traD/traD-record-evidence.yaml
entry_date: 02-DEC-2020, entry version 128. proteomes: []
file:ECOLI/traD/traD-record-evidence.yaml
entry_date: 27-NOV-2024, entry version 141. proteomes: []
The primary UniProt entry records plasmid origin. Reference-proteome membership at species or strain level does not ensure coverage of every accessory plasmid.
file:ECOLI/traD/traD-record-evidence.yaml
geneEncodingType: Plasmid
Definition: Enables the selective recruitment of a nucleoprotein complex to a type IV secretion apparatus, determining which substrates that apparatus accepts.
Justification: No existing molecular function expresses the coupling-protein role, which is the recruitment of one complex to another with plasmid-level selectivity. ATP hydrolysis is the activity the coupling protein enables, but it does not capture what the protein is for, and the C-terminal specificity determinant has no representation at all. The role is shared across a defined family whose members include TraD of F, TrwB of R388, TraG of RP4 and VirD4 of the Agrobacterium T-DNA system, so a term would serve more than one gene. Pending such a term, this review asserts ATP hydrolysis as the molecular function and records the recruitment and specificity roles in the description and process terms, rather than reaching for a binding term that would name the partner without naming the function.
Parent term: protein carrier activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Correct. Unlike many annotations of this class, the underlying location is experimentally supported rather than only inferred from the subcellular-location vocabulary: UniProt cites PMID:9324263 for the inner membrane assignment, and TraD is an integral membrane protein, not a peripheral one. Reason: The term matches the experimentally supported location. No more specific child is warranted, and the hexameric assembly at the cytoplasmic face of the pore is captured by the complex annotation instead. |
| GO:0009291 unidirectional conjugation | IMP PMID:18717787 Structural basis of specific TraD-TraM recognition during F ... | ACCEPT | Summary: Well supported. Mutations in the TraD-TraM interface are specific and required for efficient F conjugation in vivo, so the phenotype bears directly on TraD's contribution to conjugation rather than on a downstream consequence. Reason: This is the right process term for a coupling protein, and the mutant evidence is specific to the interaction surface rather than to loss of the whole protein, which makes it unusually well targeted. Retained as a core annotation. |
| GO:0016887 ATP hydrolysis activity | ISS PMID:15919815 TrwB, the coupling protein involved in DNA transport during ... | NEW | Summary: Proposed from the characterised family member rather than from an assay of TraD. TrwB, the R388 coupling protein, is a DNA-dependent ATPase that crystallises as a hexamer with a central channel, and it performs the same relaxosome-recruitment role for its plasmid that TraD performs for F. Reason: The evidence code is ISS on purpose and the supporting entity names the family member the inference comes from, so the basis stays explicit rather than being laundered into an apparent direct observation. No assay of F TraD's own nucleotide binding or hydrolysis was found. The inference is stronger here than the comparable one for F TraC, which is why a molecular function is proposed for this protein and withheld for that one: the coupling-protein family has a biochemically characterised member whose functional role matches TraD's, and the hexameric architecture is shared. |
| GO:0043684 type IV secretion system complex | TAS PMID:18717787 Structural basis of specific TraD-TraM recognition during F ... | NEW | Summary: TraD forms the cytoplasmic face of the conjugative pore, the entry point of the F-type secretion apparatus. UniProt independently records that it may form a hexamer and that it couples the transferosome to the type IV secretion system. Reason: Recorded with a traceable-author-statement code because the cited paper asserts the architecture as established background rather than determining the assembled machine itself; its own structure covers the TraD-TraM interface. Complex membership is nonetheless not in doubt, and GOA carries no cellular component for this protein beyond the membrane. |
| GO:0044097 secretion by the type IV secretion system | IMP PMID:9811665 The carboxyl terminus of protein TraD adds specificity and e... | NEW | Summary: C-terminal truncations of TraD change which relaxosomes it will serve and reduce the efficiency of F transfer, which is a direct mutant-phenotype demonstration that TraD acts in substrate delivery to the secretion system. Reason: The cargo-agnostic process term is proposed alongside, not instead of, unidirectional conjugation. The two capture different things: conjugation is the outcome for the plasmid, while this term is what TraD contributes to mechanistically, and the specificity-switching phenotype is evidence about the secretion step rather than about transfer success as such. |
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Download this section (compressed HTML)Q: Can a molecular function be defined for coupling-protein activity? TraD, TrwB, TraG and VirD4 share a role that no current GO term expresses: they recruit a specific nucleoprotein complex to a translocation apparatus. ATP hydrolysis is what they enable, not what distinguishes them.
Q: Does F TraD hydrolyse ATP, and is the activity DNA-dependent as it is for TrwB? The inference is standard but has not been tested for this protein.
Q: Should the TraD-TraI interaction be curated alongside TraD-TraM? UniProt and the literature both note an in vivo TraD-TraI contact, but only the TraM interaction is structurally resolved and annotated.
Experiment: Assay purified F TraD, or its soluble cytoplasmic domain, for ATP binding and hydrolysis in the presence and absence of single-stranded DNA, following the design used for the TrwB soluble domain. This would convert the ISS annotation proposed here into direct evidence or refute it.
Experiment: Determine whether the C-terminal specificity tail affects ATP hydrolysis as well as relaxosome selection, by comparing the activity of full-length TraD with the truncations that broaden relaxosome range. A coupling between selection and catalysis would explain why broadened specificity costs F transfer efficiency.
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