DDDA_BURC1
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 03-AUG-2022, entry version 6.
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; Proteobacteria; 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).
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};
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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 PDBsum; 6U08; -.
DR AlphaFoldDB; P0DUH5; -.
DR SMR; P0DUH5; -.
DR KEGG; bceo:I35_7839; -.
DR GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
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 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 Pfam; PF20148; DUF6531; 1.
DR Pfam; PF05488; PAAR_motif; 1.
DR Pfam; PF03527; RHS; 1.
DR Pfam; PF05593; RHS_repeat; 4.
DR Pfam; PF14428; SCP1201-deam; 1.
DR TIGRFAMs; TIGR03696; Rhs_assc_core; 1.
DR TIGRFAMs; TIGR01643; YD_repeat_2x; 7.
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"
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
