P0DUH5 · DDDA_BURC1
- ProteinDouble-stranded DNA deaminase toxin A
- GenedddA
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids1427 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
function
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. Bacteria that have this module inhibit or kill bacteria without it, giving them a growth advantage. Probably specifically inhibited by cognate immunity protein DddI (Probable). The C-terminal 163 residue fragment has double-stranded DNA cytidine deaminase activity; it does not deaminate ssDNA, ssRNA or dsRNA. Leads to C:G to T:A conversions in deaminated DNA. Preferentially deaminates 5'-TC-3' substrates (PubMed:32641830).
Catalytic activity
- a 2'-deoxycytidine in double-stranded DNA + H+ + H2O = a 2'-deoxyuridine in double-stranded DNA + NH4+
Biotechnology
The deaminase domain can be used to edit DNA. Is particularly useful for editing organellar DNA, as unlike CRISPR, it does not require guide RNA. Splitting the domain yields 2 halves that are not active until reassembled on target DNA by programmable DNA-binding proteins. Can be split at residue 1333 or 1397; each of the halves is then fused to a mitochondrial target signal, a TALE array specific for the targeted DNA, the half DddA toxin domain and a single UGI protein (uracil glycolase inhibitor), leading to editing without significant generation of insertions or deletions. Typical efficiencies on mitochondrial DNA (mtDNA) vary between 5 and 50% editing. It can be used in immortalized and non-immortalized cells, and in non-dividing cells as they continue to replicate mtDNA. A suspected tumor-related mutation in ND4 has been recreated using this system and shows the phenotypes expected for complex I disruption (PubMed:32641830).
Has also been used to edit A.thaliana chloroplast (cp) DNA. The half deaminase domain is fused to a cp target signal, a TALE array specific for the targeted DNA, the half DddA toxin domain and a UGI protein in a T-DNA construct; plants were transformed by floral dipping. The process does not require tissue culture. Three cp genes were targeted (rrn16S, psbA, rpoC1). Homoplasmic substitutions were observed in many progeny and were stably inherited (PubMed:34211131).
Has also been used to edit A.thaliana chloroplast (cp) DNA. The half deaminase domain is fused to a cp target signal, a TALE array specific for the targeted DNA, the half DddA toxin domain and a UGI protein in a T-DNA construct; plants were transformed by floral dipping. The process does not require tissue culture. Three cp genes were targeted (rrn16S, psbA, rpoC1). Homoplasmic substitutions were observed in many progeny and were stably inherited (PubMed:34211131).
Features
Showing features for binding site.
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | membrane | |
Molecular Function | hydrolase activity | |
Molecular Function | metal ion binding | |
Molecular Function | toxin activity |
Keywords
- Molecular function
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameDouble-stranded DNA deaminase toxin A
- EC number
- Short namesDddA
- Alternative names
Gene names
Organism names
- Strain
- Taxonomic lineageBacteria > Pseudomonadota > Betaproteobacteria > Burkholderiales > Burkholderiaceae > Burkholderia > Burkholderia cepacia complex
Accessions
- Primary accessionP0DUH5
Subcellular Location
UniProt Annotation
GO Annotation
Membrane ; Multi-pass membrane protein
Features
Showing features for transmembrane.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Transmembrane | 16-36 | Helical | ||||
Sequence: ALAGFLVGAVLGIALIAAVAF | ||||||
Transmembrane | 43-63 | Helical | ||||
Sequence: FGVALLAGMMAGIGAQALLSI |
Keywords
- Cellular component
Phenotypes & Variants
Disruption phenotype
A double dddA-dddI deletion has a 100-fold growth disadvantage compared to wild-type in competition experiments.
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 1347 | Not toxic against wild-type strain in competition experiments, no deamination activity, no heterologous DNA editing activity. | ||||
Sequence: E → A |
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000452477 | 1-1427 | Double-stranded DNA deaminase toxin A | |||
Sequence: MYEAARVTDPIDHTSALAGFLVGAVLGIALIAAVAFATFTCGFGVALLAGMMAGIGAQALLSIGESIGKMFSSQSGNIITGSPDVYVNSLSAAYATLSGVACSKHNPIPLVAQGSTNIFINGRPAARKDDKITCGATIGDGSHDTFFHGGTQTYLPVDDEVPPWLRTATDWAFTLAGLVGGLGGLLKASGGLSRAVLPCAAKFIGGYVLGEAFGRYVAGPAINKAIGGLFGNPIDVTTGRKILLAESETDYVIPSPLPVAIKRFYSSGIDYAGTLGRGWVLPWEIRLHARDGRLWYTDAQGRESGFPMLRAGQAAFSEADQRYLTRTPDGRYILHDLGERYYDFGQYDPESGRIAWVRRVEDQAGQWYQFERDSRGRVTEILTCGGLRAVLDYETVFGRLGTVTLVHEDERRLAVTYGYDENGQLASVTDANGAVVRQFAYTNGLMTSHMNALGFTSSYVWSKIEGEPRVVETHTSEGENWTFEYDVAGRQTRVRHADGRTAHWRFDAQSQIVEYTDLDGAFYRIKYDAVGMPVMLMLPGDRTVMFEYDDAGRIIAETDPLGRTTRTRYDGNSLRPVEVVGPDGGAWRVEYDQQGRVVSNQDSLGRENRYEYPKALTALPSAHFDALGGRKTLEWNSLGKLVGYTDCSGKTTRTSFDAFGRICSRENALGQRITYDVRPTGEPRRVTYPDGSSETFEYDAAGTLVRYIGLGGRVQELLRNARGQLIEAVDPAGRRVQYRYDVEGRLRELQQDHARYTFTYSAGGRLLTETRPDGILRRFEYGEAGELLGLDIVGAPDPHATGNRSVRTIRFERDRMGVLKVQRTPTEVTRYQHDKGDRLVKVERVPTPSGIALGIVPDAVEFEYDKGGRLVAEHGSNGSVIYTLDELDNVVSLGLPHDQTLQMLRYGSGHVHQIRFGDQVVADFERDDLHREVSRTQGRLTQRSGYDPLGRKVWQSAGIDPEMLGRGSGQLWRNYGYDGAGDLIETSDSLRGSTRFSYDPAGRLISRANPLDRKFEEFAWDAAGNLLDDAQRKSRGYVEGNRLLMWQDLRFEYDPFGNLATKRRGANQTQRFTYDGQDRLITVHTQDVRGVVETRFAYDPLGRRIAKTDTAFDLRGMKLRAETKRFVWEGLRLVQEVRETGVSSYVYSPDAPYSPVARADTVMAEALAATVIDSAKRAARIFHFHTDPVGAPQEVTDEAGEVAWAGQYAAWGKVEATNRGVTAARTDQPLRFAGQYADDSTGLHYNTFRFYDPDVGRFINQDPIGLNGGANVYHYAPNPVGWVDPWGLAGSYALGPYQISAPQLPAYNGQTVGTFYYVNDAGGLESKVFSSGGPTPYPNYANAGHVEGQSALFMRDNGISEGLVFHNNPEGTCGFCVNMTETLLPENAKMTVVPPEGAIPVKRGATGETKVFTGNSNSPKSPTKGGC |
Interaction
Subunit
The toxic domain forms a 1:1 complex with the DddI immunity protein.
Structure
Family & Domains
Features
Showing features for repeat, region, compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Repeat | 469-501 | YD 1 | ||||
Sequence: RVVETHTSEGENWTFEYDVAGRQTRVRHADGRT | ||||||
Repeat | 548-584 | YD 2 | ||||
Sequence: YDDAGRIIAETDPLGRTTRTRYDGNSLRPVEVVGPDG | ||||||
Repeat | 720-747 | YD 3 | ||||
Sequence: NARGQLIEAVDPAGRRVQYRYDVEGRLR | ||||||
Repeat | 977-1008 | YD 4 | ||||
Sequence: YDGAGDLIETSDSLRGSTRFSYDPAGRLISRA | ||||||
Region | 1264-1427 | C-terminal effector domain, has cytidine deaminase activity | ||||
Sequence: IGLNGGANVYHYAPNPVGWVDPWGLAGSYALGPYQISAPQLPAYNGQTVGTFYYVNDAGGLESKVFSSGGPTPYPNYANAGHVEGQSALFMRDNGISEGLVFHNNPEGTCGFCVNMTETLLPENAKMTVVPPEGAIPVKRGATGETKVFTGNSNSPKSPTKGGC | ||||||
Region | 1402-1427 | Disordered | ||||
Sequence: KRGATGETKVFTGNSNSPKSPTKGGC | ||||||
Compositional bias | 1409-1427 | Polar residues | ||||
Sequence: TKVFTGNSNSPKSPTKGGC |
Domain
The toxic domain is at the C-terminus (residues 1264-1427); expression of this domain in E.coli reduces viability nearly 1000-fold.
Sequence similarities
Belongs to the RHS/WapA nuclease family.
Keywords
- Domain
Family and domain databases
Sequence
- Sequence statusComplete
- Length1,427
- Mass (Da)156,702
- Last updated2021-04-07 v1
- ChecksumACA8B6DC432E9C3C
Sequence caution
Features
Showing features for compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 1409-1427 | Polar residues | ||||
Sequence: TKVFTGNSNSPKSPTKGGC |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
HG938372 EMBL· GenBank· DDBJ | CDN65395.1 EMBL· GenBank· DDBJ | Genomic DNA | Different initiation |