{"entryType":"UniProtKB reviewed (Swiss-Prot)","primaryAccession":"Q0T963","uniProtkbId":"CDIA_ECOL5","entryAudit":{"firstPublicDate":"2015-03-04","lastAnnotationUpdateDate":"2026-09-02","lastSequenceUpdateDate":"2006-09-05","entryVersion":110,"sequenceVersion":1},"annotationScore":5.0,"organism":{"scientificName":"Escherichia coli O6:K15:H31 (strain 536 / UPEC)","taxonId":362663,"lineage":["Bacteria","Pseudomonadati","Pseudomonadota","Gammaproteobacteria","Enterobacterales","Enterobacteriaceae","Escherichia"]},"proteinExistence":"1: Evidence at protein level","proteinDescription":{"recommendedName":{"fullName":{"evidences":[{"evidenceCode":"ECO:0000305"}],"value":"tRNA nuclease CdiA"},"shortNames":[{"value":"tRNase CdiA"}],"ecNumbers":[{"value":"3.1.-.-"}]},"alternativeNames":[{"fullName":{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"27531961"}],"value":"Anticodon nuclease CdiA"}},{"fullName":{"value":"CdiA-EC536"}},{"fullName":{"value":"Toxin CdiA"}}],"flag":"Precursor"},"genes":[{"geneName":{"evidences":[{"evidenceCode":"ECO:0000303","source":"PubMed","id":"21085179"}],"value":"cdiA"},"orderedLocusNames":[{"value":"ECP_4580"}]}],"comments":[{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21085179"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22333533"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"23469034"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24889811"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"25174572"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"26305955"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27531961"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27723824"}],"value":"Toxic component of a toxin-immunity protein module, which functions as a cellular contact-dependent growth inhibition (CDI) system. CDI modules allow bacteria to communicate with and inhibit the growth of closely related neighboring bacteria in a contact-dependent fashion (target cell counts decrease 100- to 1000-fold). CdiA toxicity is neutralized by its cognate immunity protein CdiI, but not by CdiI from other bacteria (PubMed:23469034, PubMed:24889811). Uses heterotrimeric OmpC and OmpF as target cell outer membrane receptors; receptor function depends on polymorphisms in extracellular loops L4 and L5 of OmpC; interacts with itself and closely related bacteria but also with OmpC from E.cloacae ATCC 13047. Its ability to preferentially bind to 'self' receptors suggests it may also play a role in self-recognition and kin selection (PubMed:27723824). A bamA mutation that decreases its expression about 5-fold is partially resistant to this strain of CdiA, probably due to decreased outer membrane receptor protein assembly (PubMed:23469034). Isolated CdiA-CT is imported in an F-pilus-mediated fashion; CdiA-CT inhibits F-mediated conjugation, probably via its N-terminus (residues 3016-3097), although it is not clear if this is physiologically significant (PubMed:24889811). Gains access to the cytoplasm of target cells by using integral inner membrane protein FtsH (PubMed:26305955). The C-terminal domain (CT) cleaves within tRNA anticodon loops (PubMed:22333533, PubMed:24889811); this activity is inhibited by cognate CdiI (PubMed:21085179, PubMed:22333533, PubMed:24889811). tRNase activity of CdiA-CT is stimulated by CysK, although the extreme C-terminus (residues 3098-3242) has tRNase activity in the absence of CysK. In vivo CDI toxicity requires CysK (PubMed:22333533, PubMed:24889811). CysK stabilizes CdiA-CT, allowing it to bind tRNA substrate; neither CdiA-CT nor CysK bind tRNA alone in vitro (PubMed:27531961). Purified CdiA-CT (residues 3016-3242) inhibits E.coli cell growth when added to cultures alone or in complex with cognate CdiI, growth is inhibited when cognate CdiI is present within the cell but not when a CdiA-CT/CdiI complex is added extracellularly, suggesting CdiA-CT alone but not the CdiA-CT/CdiI complex is imported into the target cell (PubMed:24889811)"}],"commentType":"FUNCTION"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"26305955"}],"value":"The CdiA protein is thought to be exported from the cell through the central lumen of CdiB, the other half of its two-partner system (TPS). The TPS domain probably remains associated with CdiB while the FHA-1 domain forms an extended filament with the receptor-binding domain (RBD) at its extremity; in the secretion arrested state the C-terminus of the RBD and YP domains form a hairpin-like structure as the FHA-2, PT and CT domains are periplasmic. The YP domain is probably responsible for this arrest at the point where it re-enters the host cell periplasm. Upon binding to a target cell outer membrane receptor (heterotrimeric OmpC-OmpF for this CDI) a signal is transmitted to activate secretion. The filament elongates slightly, the rest of CdiA is secreted and the FHA-2 domain becomes stably associated with the target cell's outer membrane where it facilitates entry of the toxic CT domain into the target cell periplasm. From there the toxic CT domain is cleaved and gains access to the target cell cytoplasm via an inner membrane protein (FtsH for this CDI)"}],"commentType":"FUNCTION"},{"commentType":"COFACTOR","cofactors":[{"name":"a divalent metal cation","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27531961"}],"cofactorCrossReference":{"database":"ChEBI","id":"CHEBI:60240"}}],"note":{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27531961"}],"value":"Mg(2+) and Ca(2+) support tRNase activity in vitro."}]}},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21085179"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22333533"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"27531961"}],"value":"The C-terminal (CT) domain interacts with cognate CdiI but not non-cognate CdiI from D.dadantii strain 3937 (PubMed:21085179). CdiA-CT also interacts with CysK; this is blocked upon preincubation with O-acetyl-L-serine. CysK forms a complex with CdiA-CT/CdiI (PubMed:22333533). One CdiA toxin subunit binds to each subunit of the CysK homodimer, and one CdiI immunity protein binds to each toxin subunit; the immune complex is thus a dimer of trimers. The 4 C-terminal residues of CdiA fit into the active site of CysK (PubMed:27531961)"}],"commentType":"SUBUNIT"},{"commentType":"SUBCELLULAR LOCATION","note":{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"23469034"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"25174572"},{"evidenceCode":"ECO:0000305"}],"value":"Secreted to the cell surface by CdiB, its two partner secretion pathway (TPS) partner (Probable). Expressed on the cell surface of both the encoding cell, and in mixing experiments on the target cell surface, in a proteinase K-sensitive manner. Both the N- and C-termini can be detected on target cells, whereas only the CT domain is detected in the target cell cytoplasm (PubMed:23469034). Toxin translocation into the target cell depends on the proton motive force of the target cell, but not on tolA or tonB (PubMed:25174572)"}]},"subcellularLocations":[{"location":{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"23469034"}],"value":"Secreted","id":"SL-0243"}},{"location":{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"23469034"}],"value":"Target cell membrane","id":"SL-0451"}},{"location":{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"23469034"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24889811"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"25174572"}],"value":"Target cell, target cell cytoplasm","id":"SL-0486"}}]},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"21085179"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24889811"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"26305955"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"28351921"}],"value":"The CDI activity resides in the approximately 230 residue C-terminal (CT) domain; exchanging the CT domain and cdiI gene between different strains confers resistance within cognate but not non-cognate systems (i.e. CdiI-536 / UPEC neutralizes CdiA-CT from strain 536 / UPEC but not CdiA-CT from E.coli strain EC93, Y.pestis strain CO92 or D.dadantii 3937) (PubMed:21085179). The 82 N-terminal residues (toxin import domain, residues 3016-3097) are sufficient to translocate the tRNA nuclease domain of colicin E5 into E.coli cells, probably via binding to the F pilus (PubMed:24889811). Exchanging the outer membrane receptor-binding domains between proteins exchanges the receptors recognized by CdiA. Residues 1669-2310 contribute to toxin delivery also (PubMed:28351921). The inner membrane translocation domain (IMTD) targets the toxin to a specific target cell inner membrane protein (FtsH in this case), which delivers the toxin to the target cell cytoplasm. Exchanging this IMTD between CdiA proteins alters the inner membrane protein delivery system but not the CdiI immunity protein, strongly suggesting CdiI recognizes only the toxic domain (PubMed:26305955)"}],"commentType":"DOMAIN"},{"texts":[{"evidences":[{"evidenceCode":"ECO:0000305"}],"value":"In the N-terminal section; belongs to the CdiA toxin family"}],"commentType":"SIMILARITY"}],"features":[{"type":"Signal","location":{"start":{"value":1,"modifier":"EXACT"},"end":{"value":32,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"28351921"}]},{"type":"Chain","location":{"start":{"value":33,"modifier":"EXACT"},"end":{"value":3242,"modifier":"EXACT"}},"description":"tRNA nuclease CdiA","evidences":[{"evidenceCode":"ECO:0000255"}],"featureId":"PRO_0000432088"},{"type":"Region","location":{"start":{"value":36,"modifier":"EXACT"},"end":{"value":322,"modifier":"EXACT"}},"description":"Two-partner system transport domain (TPS)","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"28351921"}]},{"type":"Region","location":{"start":{"value":351,"modifier":"EXACT"},"end":{"value":1376,"modifier":"EXACT"}},"description":"FHA-1","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"28351921"}]},{"type":"Region","location":{"start":{"value":1377,"modifier":"EXACT"},"end":{"value":1668,"modifier":"EXACT"}},"description":"Receptor-binding domain (RBD)","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"28351921"}]},{"type":"Region","location":{"start":{"value":1668,"modifier":"EXACT"},"end":{"value":1852,"modifier":"EXACT"}},"description":"YP domain","evidences":[{"evidenceCode":"ECO:0000250","source":"UniProtKB","id":"A0A1S4NYE3"}]},{"type":"Region","location":{"start":{"value":1853,"modifier":"EXACT"},"end":{"value":1913,"modifier":"EXACT"}},"description":"Periplasmic FHA-1 repeat (pFR)","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"28351921"}]},{"type":"Region","location":{"start":{"value":2021,"modifier":"EXACT"},"end":{"value":2631,"modifier":"EXACT"}},"description":"FHA-2","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"28351921"}]},{"type":"Region","location":{"start":{"value":2075,"modifier":"EXACT"},"end":{"value":2094,"modifier":"EXACT"}},"description":"Disordered","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Region","location":{"start":{"value":2310,"modifier":"EXACT"},"end":{"value":2333,"modifier":"EXACT"}},"description":"Disordered","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Region","location":{"start":{"value":2439,"modifier":"EXACT"},"end":{"value":2481,"modifier":"EXACT"}},"description":"Disordered","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Region","location":{"start":{"value":2969,"modifier":"EXACT"},"end":{"value":3242,"modifier":"EXACT"}},"description":"DUF638-CT domain; not toxic when added to the outside of E.coli, does not interfere with F-pilus mediated conjugation, toxic when expressed intracellularly","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24889811"}]},{"type":"Region","location":{"start":{"value":2972,"modifier":"EXACT"},"end":{"value":3015,"modifier":"EXACT"}},"description":"Pre-toxin (PT) domain","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"28351921"}]},{"type":"Region","location":{"start":{"value":3016,"modifier":"EXACT"},"end":{"value":3242,"modifier":"EXACT"}},"description":"CT domain; toxic when added to the outside of E.coli and when expressed intracellularly","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22333533"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24889811"}]},{"type":"Region","location":{"start":{"value":3016,"modifier":"EXACT"},"end":{"value":3097,"modifier":"EXACT"}},"description":"Toxin import domain; sufficient to import the tRNA nuclease domain of colicin E5 into E.coli, may bind F-pili","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24889811"}]},{"type":"Region","location":{"start":{"value":3020,"modifier":"EXACT"},"end":{"value":3242,"modifier":"EXACT"}},"description":"C-terminal effector domain (CT)","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"21085179"}]},{"type":"Region","location":{"start":{"value":3020,"modifier":"EXACT"},"end":{"value":3141,"modifier":"EXACT"}},"description":"Inner membrane translocation domain (IMTD), targets protein to FtsH","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"26305955"}]},{"type":"Region","location":{"start":{"value":3098,"modifier":"EXACT"},"end":{"value":3242,"modifier":"EXACT"}},"description":"tRNase function, does not interfere with F-pilus mediated conjugation","evidences":[{"evidenceCode":"ECO:0000269","source":"PubMed","id":"22333533"},{"evidenceCode":"ECO:0000269","source":"PubMed","id":"24889811"}]},{"type":"Region","location":{"start":{"value":3116,"modifier":"EXACT"},"end":{"value":3146,"modifier":"EXACT"}},"description":"Disordered","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Coiled coil","location":{"start":{"value":3137,"modifier":"EXACT"},"end":{"value":3238,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0000255"}]},{"type":"Motif","location":{"start":{"value":3016,"modifier":"EXACT"},"end":{"value":3019,"modifier":"EXACT"}},"description":"VENN CT cleavage motif","evidences":[{"evidenceCode":"ECO:0000305"}]},{"type":"Compositional bias","location":{"start":{"value":2075,"modifier":"EXACT"},"end":{"value":2091,"modifier":"EXACT"}},"description":"Basic and acidic residues","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Compositional bias","location":{"start":{"value":2322,"modifier":"EXACT"},"end":{"value":2333,"modifier":"EXACT"}},"description":"Polar residues","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Compositional bias","location":{"start":{"value":3134,"modifier":"EXACT"},"end":{"value":3146,"modifier":"EXACT"}},"description":"Basic and acidic residues","evidences":[{"evidenceCode":"ECO:0000256","source":"SAM","id":"MobiDB-lite"}]},{"type":"Active site","location":{"start":{"value":3170,"modifier":"EXACT"},"end":{"value":3170,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"27531961"}]},{"type":"Active site","location":{"start":{"value":3193,"modifier":"EXACT"},"end":{"value":3193,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"27531961"}]},{"type":"Active site","location":{"start":{"value":3196,"modifier":"EXACT"},"end":{"value":3196,"modifier":"EXACT"}},"description":"","evidences":[{"evidenceCode":"ECO:0000305","source":"PubMed","id":"27531961"}]},{"type":"Mutagenesis","location":{"start":{"value":3016,"modifier":"EXACT"},"end":{"value":3022,"modifier":"EXACT"}},"description":"No loss of toxicity when expressed as the isolated CT domain and added extracellularly to E.coli, toxic when expressed intracellularly; 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Protein is exported to the cell surface normally. 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