ID DDDA_BURC1 Reviewed; 1427 AA. AC P0DUH5; DT 07-APR-2021, integrated into UniProtKB/Swiss-Prot. DT 07-APR-2021, sequence version 1. DT 24-JAN-2024, entry version 12. DE RecName: Full=Double-stranded DNA deaminase toxin A {ECO:0000303|PubMed:32641830}; DE Short=DddA {ECO:0000303|PubMed:32641830}; DE EC=3.5.4.- {ECO:0000269|PubMed:32641830}; DE AltName: Full=Cytidine deaminase {ECO:0000303|PubMed:32641830}; DE Short=CD {ECO:0000303|PubMed:34211131}; GN Name=dddA {ECO:0000303|PubMed:32641830}; ORFNames=I35_7839; OS Burkholderia cenocepacia (strain H111). OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; OC Burkholderiaceae; Burkholderia; Burkholderia cepacia complex. OX NCBI_TaxID=1055524; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=H111; RX PubMed=24723723; DOI=10.1128/genomea.00298-14; RA Carlier A., Agnoli K., Pessi G., Suppiger A., Jenul C., Schmid N., RA Tuemmler B., Pinto-Carbo M., Eberl L.; RT "Genome Sequence of Burkholderia cenocepacia H111, a Cystic Fibrosis Airway RT Isolate."; RL Genome Announc. 2:0-0(2014). RN [2] {ECO:0007744|PDB:6U08} RP X-RAY CRYSTALLOGRAPHY (2.49 ANGSTROMS) OF 1261-1427 IN COMPLEX WITH RP IMMUNITY PROTEIN, FUNCTION AS A DS-DNA CYTIDINE DEAMINASE, FUNCTION, RP CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, SUBUNIT, DOMAIN, DISRUPTION RP PHENOTYPE, BIOTECHNOLOGY (MTDNA EDITING), AND MUTAGENESIS OF GLU-1347. RC STRAIN=H111; RX PubMed=32641830; DOI=10.1038/s41586-020-2477-4; RA Mok B.Y., de Moraes M.H., Zeng J., Bosch D.E., Kotrys A.V., Raguram A., RA Hsu F., Radey M.C., Peterson S.B., Mootha V.K., Mougous J.D., Liu D.R.; RT "A bacterial cytidine deaminase toxin enables CRISPR-free mitochondrial RT base editing."; RL Nature 583:631-637(2020). RN [3] RP BIOTECHNOLOGY (CPDNA EDITING). RX PubMed=34211131; DOI=10.1038/s41477-021-00954-6; RA Nakazato I., Okuno M., Yamamoto H., Tamura Y., Itoh T., Shikanai T., RA Takanashi H., Tsutsumi N., Arimura S.I.; RT "Targeted base editing in the plastid genome of Arabidopsis thaliana."; RL Nat. Plants 7:906-913(2021). RN [4] RP REVIEW ON SAFETY OF GENOME EDITING TOOLS. RX PubMed=36639728; DOI=10.1038/s41467-023-35886-6; RA Tao J., Bauer D.E., Chiarle R.; RT "Assessing and advancing the safety of CRISPR-Cas tools: from DNA to RNA RT editing."; RL Nat. Commun. 14:212-212(2023). CC -!- FUNCTION: Toxic component of a toxin-immunity protein module, which CC functions as a cellular contact-dependent growth inhibition (CDI) CC system. CDI modules allow bacteria to communicate with and inhibit the CC growth of closely related neighboring bacteria in a contact-dependent CC fashion. Bacteria that have this module inhibit or kill bacteria CC without it, giving them a growth advantage. Probably specifically CC inhibited by cognate immunity protein DddI (Probable). The C-terminal CC 163 residue fragment has double-stranded DNA cytidine deaminase CC activity; it does not deaminate ssDNA, ssRNA or dsRNA. Leads to C:G to CC T:A conversions in deaminated DNA. Preferentially deaminates 5'-TC-3' CC substrates (PubMed:32641830). {ECO:0000269|PubMed:32641830, CC ECO:0000305}. CC -!- CATALYTIC ACTIVITY: CC Reaction=a 2'-deoxycytidine in double-stranded DNA + H(+) + H2O = a 2'- CC deoxyuridine in double-stranded DNA + NH4(+); Xref=Rhea:RHEA:66604, CC Rhea:RHEA-COMP:17070, Rhea:RHEA-COMP:17071, ChEBI:CHEBI:15377, CC ChEBI:CHEBI:15378, ChEBI:CHEBI:28938, ChEBI:CHEBI:85452, CC ChEBI:CHEBI:133902; Evidence={ECO:0000269|PubMed:32641830}; CC -!- SUBUNIT: The toxic domain forms a 1:1 complex with the DddI immunity CC protein. {ECO:0000269|PubMed:32641830}. CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000255}; Multi-pass membrane CC protein {ECO:0000255}. CC -!- DOMAIN: The toxic domain is at the C-terminus (residues 1264-1427); CC expression of this domain in E.coli reduces viability nearly 1000-fold. CC {ECO:0000269|PubMed:32641830}. CC -!- DISRUPTION PHENOTYPE: A double dddA-dddI deletion has a 100-fold growth CC disadvantage compared to wild-type in competition experiments. CC {ECO:0000269|PubMed:32641830}. CC -!- BIOTECHNOLOGY: The deaminase domain can be used to edit DNA. Is CC particularly useful for editing organellar DNA, as unlike CRISPR, it CC does not require guide RNA. Splitting the domain yields 2 halves that CC are not active until reassembled on target DNA by programmable DNA- CC binding proteins. Can be split at residue 1333 or 1397; each of the CC halves is then fused to a mitochondrial target signal, a TALE array CC specific for the targeted DNA, the half DddA toxin domain and a single CC UGI protein (uracil glycolase inhibitor), leading to editing without CC significant generation of insertions or deletions. Typical efficiencies CC on mitochondrial DNA (mtDNA) vary between 5 and 50% editing. It can be CC used in immortalized and non-immortalized cells, and in non-dividing CC cells as they continue to replicate mtDNA. A suspected tumor-related CC mutation in ND4 has been recreated using this system and shows the CC phenotypes expected for complex I disruption (PubMed:32641830). Has CC also been used to edit A.thaliana chloroplast (cp) DNA. The half CC deaminase domain is fused to a cp target signal, a TALE array specific CC for the targeted DNA, the half DddA toxin domain and a UGI protein in a CC T-DNA construct; plants were transformed by floral dipping. The process CC does not require tissue culture. Three cp genes were targeted (rrn16S, CC psbA, rpoC1). Homoplasmic substitutions were observed in many progeny CC and were stably inherited (PubMed:34211131). CC {ECO:0000269|PubMed:32641830, ECO:0000269|PubMed:34211131}. CC -!- SIMILARITY: Belongs to the RHS/WapA nuclease family. {ECO:0000305}. CC -!- SEQUENCE CAUTION: CC Sequence=CDN65395.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; HG938372; CDN65395.1; ALT_INIT; Genomic_DNA. DR RefSeq; WP_006498588.1; NZ_HG938372.1. DR PDB; 6U08; X-ray; 2.49 A; A/C/E/G=1261-1427. DR PDB; 8E5D; X-ray; 2.39 A; A=1290-1422. DR PDB; 8E5E; X-ray; 2.62 A; A=1290-1422. DR PDBsum; 6U08; -. DR PDBsum; 8E5D; -. DR PDBsum; 8E5E; -. DR AlphaFoldDB; P0DUH5; -. DR SMR; P0DUH5; -. DR KEGG; bceo:I35_7839; -. DR GO; GO:0016020; C:membrane; IEA:UniProtKB-SubCell. DR GO; GO:0016787; F:hydrolase activity; IEA:UniProtKB-KW. DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW. DR GO; GO:0090729; F:toxin activity; IEA:UniProtKB-KW. DR CDD; cd14742; PAAR_RHS; 1. DR Gene3D; 2.60.200.60; -; 1. DR Gene3D; 3.90.930.1; -; 1. DR Gene3D; 2.180.10.10; RHS repeat-associated core; 2. DR InterPro; IPR032724; DddA-like. DR InterPro; IPR045351; DUF6531. DR InterPro; IPR008727; PAAR_motif. DR InterPro; IPR001826; RHS. DR InterPro; IPR022385; Rhs_assc_core. DR InterPro; IPR031325; RHS_repeat. DR InterPro; IPR006530; YD. DR NCBIfam; TIGR03696; Rhs_assc_core; 1. DR NCBIfam; TIGR01643; YD_repeat_2x; 7. DR PANTHER; PTHR32305; -; 1. DR PANTHER; PTHR32305:SF15; PROTEIN RHSA-RELATED; 1. DR Pfam; PF14428; DddA-like; 1. DR Pfam; PF20148; DUF6531; 1. DR Pfam; PF05488; PAAR_motif; 1. DR Pfam; PF03527; RHS; 1. DR Pfam; PF05593; RHS_repeat; 8. PE 1: Evidence at protein level; KW 3D-structure; Hydrolase; Membrane; Metal-binding; Repeat; Toxin; KW Transmembrane; Transmembrane helix; Zinc. FT CHAIN 1..1427 FT /note="Double-stranded DNA deaminase toxin A" FT /id="PRO_0000452477" FT TRANSMEM 16..36 FT /note="Helical" FT /evidence="ECO:0000255" FT TRANSMEM 43..63 FT /note="Helical" FT /evidence="ECO:0000255" FT REPEAT 469..501 FT /note="YD 1" FT /evidence="ECO:0000255" FT REPEAT 548..584 FT /note="YD 2" FT /evidence="ECO:0000255" FT REPEAT 720..747 FT /note="YD 3" FT /evidence="ECO:0000255" FT REPEAT 977..1008 FT /note="YD 4" FT /evidence="ECO:0000255" FT REGION 1264..1427 FT /note="C-terminal effector domain, has cytidine deaminase FT activity" FT /evidence="ECO:0000269|PubMed:32641830" FT REGION 1402..1427 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 1409..1427 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT BINDING 1345 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0007744|PDB:6U08" FT BINDING 1373 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0007744|PDB:6U08" FT BINDING 1376 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0007744|PDB:6U08" FT MUTAGEN 1347 FT /note="E->A: Not toxic against wild-type strain in FT competition experiments, no deamination activity, no FT heterologous DNA editing activity." FT /evidence="ECO:0000269|PubMed:32641830" FT STRAND 1291..1294 FT /evidence="ECO:0007829|PDB:8E5D" FT STRAND 1297..1300 FT /evidence="ECO:0007829|PDB:8E5D" FT STRAND 1308..1310 FT /evidence="ECO:0007829|PDB:8E5D" FT STRAND 1312..1318 FT /evidence="ECO:0007829|PDB:8E5D" FT STRAND 1320..1322 FT /evidence="ECO:0007829|PDB:8E5E" FT STRAND 1324..1331 FT /evidence="ECO:0007829|PDB:8E5D" FT TURN 1341..1344 FT /evidence="ECO:0007829|PDB:8E5D" FT HELIX 1346..1357 FT /evidence="ECO:0007829|PDB:8E5D" FT STRAND 1361..1366 FT /evidence="ECO:0007829|PDB:8E5D" FT HELIX 1374..1383 FT /evidence="ECO:0007829|PDB:8E5D" FT STRAND 1389..1393 FT /evidence="ECO:0007829|PDB:8E5D" FT STRAND 1406..1408 FT /evidence="ECO:0007829|PDB:8E5D" FT STRAND 1410..1413 FT /evidence="ECO:0007829|PDB:8E5D" SQ SEQUENCE 1427 AA; 156702 MW; ACA8B6DC432E9C3C CRC64; MYEAARVTDP IDHTSALAGF LVGAVLGIAL IAAVAFATFT CGFGVALLAG MMAGIGAQAL LSIGESIGKM FSSQSGNIIT GSPDVYVNSL SAAYATLSGV ACSKHNPIPL VAQGSTNIFI NGRPAARKDD KITCGATIGD GSHDTFFHGG TQTYLPVDDE VPPWLRTATD WAFTLAGLVG GLGGLLKASG GLSRAVLPCA AKFIGGYVLG EAFGRYVAGP AINKAIGGLF GNPIDVTTGR KILLAESETD YVIPSPLPVA IKRFYSSGID YAGTLGRGWV LPWEIRLHAR DGRLWYTDAQ GRESGFPMLR AGQAAFSEAD QRYLTRTPDG RYILHDLGER YYDFGQYDPE SGRIAWVRRV EDQAGQWYQF ERDSRGRVTE ILTCGGLRAV LDYETVFGRL GTVTLVHEDE RRLAVTYGYD ENGQLASVTD ANGAVVRQFA YTNGLMTSHM NALGFTSSYV WSKIEGEPRV VETHTSEGEN WTFEYDVAGR QTRVRHADGR TAHWRFDAQS QIVEYTDLDG AFYRIKYDAV GMPVMLMLPG DRTVMFEYDD AGRIIAETDP LGRTTRTRYD GNSLRPVEVV GPDGGAWRVE YDQQGRVVSN QDSLGRENRY EYPKALTALP SAHFDALGGR KTLEWNSLGK LVGYTDCSGK TTRTSFDAFG RICSRENALG QRITYDVRPT GEPRRVTYPD GSSETFEYDA AGTLVRYIGL GGRVQELLRN ARGQLIEAVD PAGRRVQYRY DVEGRLRELQ QDHARYTFTY SAGGRLLTET RPDGILRRFE YGEAGELLGL DIVGAPDPHA TGNRSVRTIR FERDRMGVLK VQRTPTEVTR YQHDKGDRLV KVERVPTPSG IALGIVPDAV EFEYDKGGRL VAEHGSNGSV IYTLDELDNV VSLGLPHDQT LQMLRYGSGH VHQIRFGDQV VADFERDDLH REVSRTQGRL TQRSGYDPLG RKVWQSAGID PEMLGRGSGQ LWRNYGYDGA GDLIETSDSL RGSTRFSYDP AGRLISRANP LDRKFEEFAW DAAGNLLDDA QRKSRGYVEG NRLLMWQDLR FEYDPFGNLA TKRRGANQTQ RFTYDGQDRL ITVHTQDVRG VVETRFAYDP LGRRIAKTDT AFDLRGMKLR AETKRFVWEG LRLVQEVRET GVSSYVYSPD APYSPVARAD TVMAEALAAT VIDSAKRAAR IFHFHTDPVG APQEVTDEAG EVAWAGQYAA WGKVEATNRG VTAARTDQPL RFAGQYADDS TGLHYNTFRF YDPDVGRFIN QDPIGLNGGA NVYHYAPNPV GWVDPWGLAG SYALGPYQIS APQLPAYNGQ TVGTFYYVND AGGLESKVFS SGGPTPYPNY ANAGHVEGQS ALFMRDNGIS EGLVFHNNPE GTCGFCVNMT ETLLPENAKM TVVPPEGAIP VKRGATGETK VFTGNSNSPK SPTKGGC //