id: P41067 gene_symbol: traB product_type: PROTEIN status: DRAFT taxon: id: NCBITaxon:83333 label: Escherichia coli K-12 description: >- TraB is a structural subunit of the outer-membrane core complex of the F-type type IV secretion system, encoded on the F plasmid and on the related IncFII plasmid ColB2 rather than on the chromosome. It is the VirB10 counterpart of that machine. In the cryo-EM structure of an F-family core complex, TraB forms the central cone as a seventeen-fold symmetrical ring of beta-barrels, seated inside an outer ring built from TraK and TraV; the cone is the passage through which the machine's substrate and its pilus reach the cell surface. TraB is required for assembly of the F pilus, the extracellular filament that establishes contact with a recipient cell, and so for conjugative transfer. Its role is architectural: it holds the core complex together across the symmetry mismatch between the outer ring and the cone, and it contributes no catalytic activity of its own. reference_proteome_assessments: - reference_proteomes: - UP000000625 status: NO_SUPPORTED_COUNTERPART reviewed_on: '2026-10-19' reason: Retain P41067 as the primary Swiss-Prot accession. No significant reference-proteome hit was returned. The reviewed entry explicitly cites F and ColB2 plasmids, making accessory-replicon differences relevant. The negative result applies to the searched reference proteome, not all E. coli strains or plasmids. evidence: - type: PROTEOME_SEARCH description: 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. supported_by: - reference_id: file:ECOLI/traB/traB-record-evidence.yaml supporting_text: 'target_sequence_count: 4403' - reference_id: file:ECOLI/traB/traB-record-evidence.yaml supporting_text: 'candidate_count: 0' - type: PROTEOME_MEMBERSHIP description: The primary accession is outside every searched exact-taxon reference proteome. supported_by: - reference_id: file:ECOLI/traB/traB-record-evidence.yaml supporting_text: 'primary_in_any_reference_proteome: false' - type: RECORD_HISTORY description: 'Sampled UniSave observations: 16-SEP-2015, entry version 71.: no Proteomes cross-reference; 12-AUG-2020, entry version 85.: no Proteomes cross-reference; 27-NOV-2024, entry version 97.: no Proteomes cross-reference. These dated observations do not establish uninterrupted membership/absence, the exact change date, or UniProt''s motivation.' supported_by: - reference_id: file:ECOLI/traB/traB-record-evidence.yaml supporting_text: |- entry_date: 16-SEP-2015, entry version 71. proteomes: [] - reference_id: file:ECOLI/traB/traB-record-evidence.yaml supporting_text: |- entry_date: 12-AUG-2020, entry version 85. proteomes: [] - reference_id: file:ECOLI/traB/traB-record-evidence.yaml supporting_text: |- entry_date: 27-NOV-2024, entry version 97. proteomes: [] - type: CURATION_CONTEXT description: The primary UniProt entry records plasmid origin. Reference-proteome membership at species or strain level does not ensure coverage of every accessory plasmid. supported_by: - reference_id: file:ECOLI/traB/traB-record-evidence.yaml supporting_text: 'geneEncodingType: Plasmid' references: - id: file:ECOLI/traB/traB-record-evidence.yaml title: Compact archived record and sequence evidence for P41067 - id: PMID:35046412 title: Structure of a type IV secretion system core complex encoded by multi-drug resistance F plasmids. findings: - statement: >- The F-type outer-membrane core complex is built from an outer ring of TraK and TraV C-terminal domains and a central cone made entirely of TraB beta-barrels, establishing TraB as a structural subunit of the complex. supporting_text: The OMCCF consists of a 13-fold symmetrical outer ring complex (ORC) built from 26 copies of TraK and TraV C-terminal domains, and a 17-fold symmetrical central cone (CC) composed of 17 copies of TraB β-barrels. - statement: >- TraB's domains are functionally load-bearing for the secretion system, not incidental to it. supporting_text: define the importance of TraK, TraV and TraB domains to T4SSF function reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Verified against the cached record. The structure was solved for pED208, an F-family plasmid, so it establishes the role for the F-type system rather than for this exact polypeptide; that scope limit is stated in the notes and in the core function's reason. - id: PMID:7915817 title: Analysis of the sequence and gene products of the transfer region of the F sex factor. findings: - statement: >- The F transfer region is the reference conjugation system, and its genes cover pilus synthesis, mating-pair stabilization, surface exclusion, DNA nicking and transfer, and regulation. TraB belongs to the pilus-synthesis group. supporting_text: These are involved in the synthesis of pili, extracellular filaments which establish contact between donor and recipient cells; mating-pair stabilization; prevention of mating between similar donor cells in a process termed surface exclusions; DNA nicking and transfer during conjugation; and the regulation of expression of these functions. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- The standard compendium of the F transfer region, used here for the system-level context rather than for a TraB-specific claim. Cached record is abstract-only. - id: PMID:20172994 title: Biochemical dissection of the ATPase TraB, the VirB4 homologue of the Escherichia coli pKM101 conjugation machinery. findings: - statement: >- The protein characterized in this paper is the VirB4 homologue of the pKM101 conjugation system, not the F-plasmid TraB that carries accession P41067. supporting_text: a VirB4 homologue from the pKM101 conjugation - statement: >- Even for the pKM101 protein, ATP hydrolysis depended on how the protein was prepared: the membrane-derived form did not hydrolyse ATP and only the soluble hexamer did. supporting_text: TraB can form hexamers capable of hydrolyzing ATP. reference_review: relevance: LOW correctness: MISCITED review_notes: >- Correct identifier and title, but the paper does not support the claim made for this gene product. Its subject is the pKM101 VirB4 homologue, which has its own UniProt entry Q46698 (866 aa, TrbE/VirB4 family). P41067 is 475 aa, belongs to the TraB family, and is encoded on plasmid F and ColB2; F's own VirB4-family ATPase is the separate gene product TraC (P18004). The two proteins share only a gene symbol, because Tra symbols are not stable between conjugative plasmids. - id: file:ECOLI/traB/traB-hypotheses/function-hypothesis-go-0016887/openscientist.md title: OpenScientist hypothesis report for traB ATP hydrolysis activity publication_type: DEEP_RESEARCH findings: - statement: >- OpenScientist refuted ATP hydrolysis activity for P41067 and traced the IDA to a TraB name collision with the pKM101 VirB4-family ATPase. supporting_text: 'P41067 lacks a Walker-A / P-loop motif' existing_annotations: - term: id: GO:0016887 label: ATP hydrolysis activity evidence_type: IDA original_reference_id: PMID:20172994 qualifier: enables review: summary: >- This annotation is attributed to the wrong protein. The cited paper characterizes the VirB4 homologue of the pKM101 conjugation system, which its abstract states outright, and that protein has its own UniProt entry (Q46698, 866 aa, TrbE/VirB4 family). P41067 is the 475 aa TraB of plasmid F and ColB2, assigned by UniProt to the TraB family, and the F plasmid's own VirB4-family ATPase is a different gene product, TraC (P18004). The structural evidence for P41067 places it in the outer-membrane core complex as the central-cone beta-barrel subunit, a role with no ATPase activity. The collision is nomenclatural: on pKM101 the symbol TraB names the protein that on F is called TraC. action: REMOVE reason: >- Removal here is not second-guessing an assay whose full text is unavailable, which is the case that calls for UNDECIDED. The cached abstract explicitly names the plasmid and the protein family, which is the condition under which a reference-scope objection is warranted, and four independent facts separate the two proteins: plasmid of origin, protein family, length, and the fact that F already assigns the VirB4-family role to TraC. Retaining the annotation would give a structural subunit a catalytic activity that no experiment on it supports, and would leave the F-type core complex looking as though it contained two VirB4-family ATPases. An independent OpenScientist function-assignment run reached the same conclusion from sequence: P41067 is in the VirB10/TraB/TrbI family and lacks a Walker-A motif, so it cannot hydrolyse ATP. supported_by: - reference_id: PMID:20172994 supporting_text: Biochemical dissection of the ATPase TraB, the VirB4 homologue of the Escherichia coli pKM101 conjugation machinery. - reference_id: file:ECOLI/traB/traB-hypotheses/function-hypothesis-go-0016887/openscientist.md supporting_text: P41067 lacks a Walker-A / P-loop motif source_defects: - defect_type: WRONG_GENE_PRODUCT resource: CACAO slot: DB_Object_ID requested_change: REPOINT asserted_value: UniProtKB:P41067 corrected_value: UniProtKB:Q46698 corrected_label: TraB of plasmid pKM101, VirB4-family ATPase (866 aa) cause: SYMBOL_COLLISION confidence: CONFIRMED explanation: >- This CACAO IDA row (2015-03-20) gives ATP hydrolysis activity to P41067, the 475 aa TraB of plasmid F (VirB10/TraB family, no Walker-A motif). The cited paper (PMID:20172994) assays the VirB4 homologue of plasmid pKM101, which is also named TraB and has its own UniProt entry, Q46698 (866 aa, plasmid pKM101). On F the VirB4-family ATPase is TraC (P18004). The row should be moved to Q46698. - term: id: GO:0005198 label: structural molecule activity evidence_type: ISS original_reference_id: PMID:35046412 qualifier: enables review: summary: >- The cryo-EM structure of an F-family outer-membrane core complex resolves TraB as a seventeen-fold ring of beta-barrels forming the central cone, with no catalytic role. A structural molecular function is the accurate description of what this protein does. action: NEW reason: >- Proposed rather than asserted from a direct assay on this polypeptide. The structure was solved for pED208, an F-family plasmid, so the evidence code is ISS rather than IDA. The protein currently has no correct molecular function annotation at all, its one GOA row being an ATPase activity attributed from a different plasmid's protein, so this fills a real gap rather than adding a redundant term. - term: id: GO:0043684 label: type IV secretion system complex evidence_type: ISS original_reference_id: PMID:35046412 qualifier: part_of review: summary: >- TraB is one of the three proteins that build the F-type outer-membrane core complex, contributing the central cone within the TraK and TraV outer ring. action: NEW reason: >- Complex membership is read directly off the solved architecture of the F-family core complex. ISS rather than IDA because the structure is of a homolog from a related F-family plasmid, not of this polypeptide. - term: id: GO:0009279 label: cell outer membrane evidence_type: ISS original_reference_id: PMID:35046412 qualifier: located_in review: summary: >- The structure places TraB's beta-barrels in the outer-membrane core complex. No subcellular location is currently annotated for this protein from any source. action: NEW reason: >- Proposed conservatively and as the only location asserted. VirB10-family proteins are generally also anchored in the inner membrane, but no F-specific experiment establishes that for this protein, so a second location is left for the suggested experiments rather than annotated here. - term: id: GO:0044097 label: secretion by the type IV secretion system evidence_type: ISS original_reference_id: PMID:35046412 qualifier: involved_in review: summary: >- TraB's domains are functionally important to the F-type secretion system, and it contributes the cone through which the machine reaches the surface. action: NEW reason: >- The cargo-agnostic parent term is used deliberately in preference to GO:0009291 unidirectional conjugation. The structural evidence supports TraB's participation in the secretion machinery; attributing the conjugation outcome to it would need F-specific mutant data, which is raised as a question instead. core_functions: - description: >- Structural subunit of the outer-membrane core complex of the F-type type IV secretion system. TraB oligomerizes into the seventeen-fold central cone of beta-barrels that sits within the TraK and TraV outer ring, holding the complex together across the symmetry mismatch between the two substructures and forming the passage through which the machine reaches the cell surface. This architectural contribution is what makes the assembled apparatus, and hence conjugative transfer, possible; TraB itself performs no chemistry. molecular_function: id: GO:0005198 label: structural molecule activity directly_involved_in: - id: GO:0044097 label: secretion by the type IV secretion system in_complex: id: GO:0043684 label: type IV secretion system complex locations: - id: GO:0009279 label: cell outer membrane supported_by: - reference_id: PMID:35046412 supporting_text: The OMCCF consists of a 13-fold symmetrical outer ring complex (ORC) built from 26 copies of TraK and TraV C-terminal domains, and a 17-fold symmetrical central cone (CC) composed of 17 copies of TraB β-barrels. - reference_id: PMID:35046412 supporting_text: define the importance of TraK, TraV and TraB domains to T4SSF function suggested_questions: - question: >- Should GO:0009297 pilus assembly be annotated to F TraB? UniProt states that the protein is involved in F pilus assembly, but GOA carries no biological process annotation for it at all, so the statement has never been captured. - question: >- Does F TraB span both membranes? The core-complex structure places its beta-barrels in the outer membrane, while VirB10-family proteins are generally anchored in the inner membrane and reach the outer one. No subcellular location is annotated for P41067 from an F-specific experiment. - question: >- How many other GOA rows on conjugative plasmid gene products have been attributed across plasmids because Tra symbols are reused? This annotation was found by checking one protein; the same collision pattern could affect others, TraC and TraB on F and pKM101 being the clearest pair. suggested_experiments: - description: >- Test directly whether purified F TraB (P41067) hydrolyses ATP, under both the membrane-derived and soluble preparations that gave different answers for the pKM101 VirB4 homologue. A negative result on the F protein would close the question this review had to settle by sequence and family argument alone. - description: >- Determine the subcellular topology of F TraB by protease accessibility or fractionation in an F-plasmid-bearing K-12 strain, to establish whether it is anchored in the inner membrane as VirB10-family proteins are while contributing beta-barrels to the outer-membrane cone.