DRA2B_DEIRA
ID DRA2B_DEIRA Reviewed; 408 AA.
AC Q7DF80; O83029; Q9RU04;
DT 25-MAY-2022, integrated into UniProtKB/Swiss-Prot.
DT 18-APR-2012, sequence version 1.
DT 03-AUG-2022, entry version 47.
DE RecName: Full=RNA-guided DNA endonuclease TnpB {ECO:0000303|PubMed:34619744};
DE EC=3.1.21.- {ECO:0000269|PubMed:34619744};
GN Name=tnpB {ECO:0000303|PubMed:20090938};
GN Synonyms=orf2 {ECO:0000303|PubMed:10567266},
GN tnpC {ECO:0000312|EMBL:BAA32390.1};
GN OrderedLocusNames=DR_0666 {ECO:0000312|EMBL:AAF10241.1};
GN and
GN OrderedLocusNames=DR_0978 {ECO:0000312|EMBL:AAF10555.1};
GN and
GN OrderedLocusNames=DR_1381 {ECO:0000312|EMBL:AAF10952.1};
GN and
GN OrderedLocusNames=DR_1593 {ECO:0000312|EMBL:AAF11156.1};
GN and
GN OrderedLocusNames=DR_1651 {ECO:0000312|EMBL:AAF11208.1};
GN and
GN OrderedLocusNames=DR_1933 {ECO:0000312|EMBL:AAF11486.1};
GN and
GN OrderedLocusNames=DR_2324 {ECO:0000312|EMBL:AAF11872.1};
OS Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG
OS 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422).
OC Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae;
OC Deinococcus.
OX NCBI_TaxID=243230;
RN [1] {ECO:0000312|EMBL:BAA32390.1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], INSERTION SITE, AND NOMENCLATURE IS8301.
RC STRAIN=R1 / KD8301;
RX PubMed=14676423; DOI=10.1266/ggs.78.319;
RA Islam S.M., Hua Y., Ohba H., Satoh K., Kikuchi M., Yanagisawa T.,
RA Narumi I.;
RT "Characterization and distribution of IS8301 in the radioresistant
RT bacterium Deinococcus radiodurans.";
RL Genes Genet. Syst. 78:319-327(2003).
RN [2] {ECO:0000312|EMBL:AAF11208.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=10567266; DOI=10.1126/science.286.5444.1571;
RA White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D.,
RA Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L.,
RA Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M.,
RA Vamathevan J.J., Lam P., McDonald L.A., Utterback T.R., Zalewski C.,
RA Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D.,
RA Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C.,
RA Fraser C.M.;
RT "Genome sequence of the radioresistant bacterium Deinococcus radiodurans
RT R1.";
RL Science 286:1571-1577(1999).
RN [3]
RP FUNCTION, TRANSPOSITION, INDUCTION BY DNA DAMAGE, AND NOMENCLATURE ISDRA2.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=16359337; DOI=10.1111/j.1365-2958.2005.04936.x;
RA Mennecier S., Servant P., Coste G., Bailone A., Sommer S.;
RT "Mutagenesis via IS transposition in Deinococcus radiodurans.";
RL Mol. Microbiol. 59:317-325(2006).
RN [4]
RP FUNCTION, REACTION MECHANISM, TRANSPOSITION, INDUCTION BY IRRADIATION, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=R1 / ISDra2f;
RX PubMed=20090938; DOI=10.1371/journal.pgen.1000799;
RA Pasternak C., Ton-Hoang B., Coste G., Bailone A., Chandler M., Sommer S.;
RT "Irradiation-induced Deinococcus radiodurans genome fragmentation triggers
RT transposition of a single resident insertion sequence.";
RL PLoS Genet. 6:e1000799-e1000799(2010).
RN [5]
RP DISRUPTION PHENOTYPE, AND MUTAGENESIS OF 331-CYS--CYS-334 AND
RP 351-CYS--CYS-354.
RC STRAIN=R1 / ISDra2f;
RX PubMed=23461641; DOI=10.1111/mmi.12194;
RA Pasternak C., Dulermo R., Ton-Hoang B., Debuchy R., Siguier P., Coste G.,
RA Chandler M., Sommer S.;
RT "ISDra2 transposition in Deinococcus radiodurans is downregulated by
RT TnpB.";
RL Mol. Microbiol. 88:443-455(2013).
RN [6]
RP FUNCTION AS DSDNA ENDONUCLEASE, PROBABLE ACTIVE SITE, BIOTECHNOLOGY,
RP RNA-BINDING, AND MUTAGENESIS OF ASP-191.
RX PubMed=34619744; DOI=10.1038/s41586-021-04058-1;
RA Karvelis T., Druteika G., Bigelyte G., Budre K., Zedaveinyte R.,
RA Silanskas A., Kazlauskas D., Venclovas C., Siksnys V.;
RT "Transposon-associated TnpB is a programmable RNA-guided DNA
RT endonuclease.";
RL Nature 599:692-696(2021).
CC -!- FUNCTION: An RNA-guided dsDNA endonuclease. When guided by an RNA
CC derived from the right-end element of its insertion sequence element
CC (IS), cleaves DNA downstream of the 5'-TTGAT-3' transposon-associated
CC motif (TAM). Cleaves supercoiled and linear DNA in a staggered manner
CC 15-21 bases from the TAM yielding 5'-overhangs. Binds reRNA, an
CC approximately 150 nucleotide base sRNA derived from the 3' end of its
CC own gene, the right end (RE) of the insertion sequence (IS) and
CC sequence downstream of the IS (PubMed:34619744). May cleave at the
CC donor joint (generated by ISDra2 excision mediated by TnpA) to trigger
CC homology-directed repair and restore intact IS in its original position
CC (Probable). Inhibits transposition activity of the IS200 element; the
CC possible zinc-binding motif of TnpB is required for this inhibition
CC (PubMed:23461641). Part of IS element ISDra2, this protein is not
CC required for transposition (PubMed:20090938). The IS element inserts 3'
CC of the sequence 5'-TTGAT-3'; target duplication has not been observed
CC (PubMed:14676423, PubMed:16359337). {ECO:0000269|PubMed:14676423,
CC ECO:0000269|PubMed:16359337, ECO:0000269|PubMed:20090938,
CC ECO:0000269|PubMed:23461641, ECO:0000269|PubMed:34619744,
CC ECO:0000305|PubMed:34619744}.
CC -!- SUBUNIT: Monomer. {ECO:0000305|PubMed:34619744}.
CC -!- DISRUPTION PHENOTYPE: When tested in an R1 strain with only a single
CC IS200 element (DR_1651 and DR_1652), not required for transposition of
CC this IS element. Single tnpA or double tnpA-tnpB deletion leads to loss
CC of transposition. {ECO:0000269|PubMed:20090938,
CC ECO:0000269|PubMed:23461641}.
CC -!- BIOTECHNOLOGY: Has been shown to cleave dsDNA in a targeted manner in
CC human (HEK293T) cells, suggesting it could be used for genome editing.
CC {ECO:0000269|PubMed:34619744}.
CC -!- MISCELLANEOUS: Belongs to the IS200/IS605 insertion sequence (IS)
CC element family, formerly called IS8301 (PubMed:14676423,
CC PubMed:20090938). This element is subject to strain polymorphism; in
CC the ATCC 13939 / R1 strain genome sequenced by White there are 7
CC complete and 1 incomplete IS200/IS605 elements (PubMed:10567266).
CC Another R1 strain has only 1 copy of this element (PubMed:14676423,
CC PubMed:20090938). Another group found 2 copies of this element in
CC untreated R1 strains (PubMed:16359337, PubMed:10567266,
CC PubMed:14676423, PubMed:20090938). {ECO:0000269|PubMed:10567266,
CC ECO:0000269|PubMed:14676423, ECO:0000269|PubMed:16359337,
CC ECO:0000269|PubMed:20090938, ECO:0000303|PubMed:14676423,
CC ECO:0000303|PubMed:20090938}.
CC -!- MISCELLANEOUS: This class of protein is thought to probably be the
CC ancestor of Cas9 and Cas12 CRISPR endonucleases.
CC {ECO:0000305|PubMed:34619744}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the transposase 2
CC family. {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the transposase 35
CC family. {ECO:0000305}.
CC -!- CAUTION: Has been suggested to both inhibit transposition and possibly
CC enhance transposition. {ECO:0000269|PubMed:23461641,
CC ECO:0000305|PubMed:34619744}.
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DR EMBL; AB016803; BAA32390.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF10241.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF10555.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF10952.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF11156.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF11208.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF11486.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF11872.1; -; Genomic_DNA.
DR PIR; E75452; E75452.
DR PIR; G75376; G75376.
DR RefSeq; NP_294389.1; NC_001263.1.
DR RefSeq; NP_294702.1; NC_001263.1.
DR RefSeq; NP_295104.1; NC_001263.1.
DR RefSeq; NP_295316.1; NC_001263.1.
DR RefSeq; NP_295374.1; NC_001263.1.
DR RefSeq; NP_295656.1; NC_001263.1.
DR RefSeq; NP_296045.1; NC_001263.1.
DR RefSeq; WP_010887311.1; NZ_CP015081.1.
DR RefSeq; WP_010888231.1; NC_001263.1.
DR STRING; 243230.DR_0666; -.
DR DNASU; 1800418; -.
DR EnsemblBacteria; AAF10241; AAF10241; DR_0666.
DR EnsemblBacteria; AAF10555; AAF10555; DR_0978.
DR EnsemblBacteria; AAF10952; AAF10952; DR_1381.
DR EnsemblBacteria; AAF11156; AAF11156; DR_1593.
DR EnsemblBacteria; AAF11208; AAF11208; DR_1651.
DR EnsemblBacteria; AAF11486; AAF11486; DR_1933.
DR EnsemblBacteria; AAF11872; AAF11872; DR_2324.
DR KEGG; dra:DR_0666; -.
DR KEGG; dra:DR_0978; -.
DR KEGG; dra:DR_1381; -.
DR KEGG; dra:DR_1593; -.
DR KEGG; dra:DR_1651; -.
DR KEGG; dra:DR_1933; -.
DR KEGG; dra:DR_2324; -.
DR PATRIC; fig|243230.17.peg.1165; -.
DR eggNOG; COG0675; Bacteria.
DR HOGENOM; CLU_032903_0_0_0; -.
DR InParanoid; Q7DF80; -.
DR OMA; NEYQDEH; -.
DR OrthoDB; 222391at2; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0032196; P:transposition; IEA:UniProtKB-KW.
DR InterPro; IPR037278; ARFGAP/RecO.
DR InterPro; IPR001959; Transposase_2.
DR InterPro; IPR010095; Transposase_IS605_OrfB_C.
DR InterPro; IPR021027; Transposase_put_HTH.
DR Pfam; PF12323; HTH_OrfB_IS605; 1.
DR Pfam; PF01385; OrfB_IS605; 1.
DR Pfam; PF07282; OrfB_Zn_ribbon; 1.
DR SUPFAM; SSF57863; SSF57863; 1.
DR TIGRFAMs; TIGR01766; tspaseT_teng_C; 1.
PE 1: Evidence at protein level;
KW DNA recombination; DNA-binding; Endonuclease; Hydrolase; Metal-binding;
KW Nuclease; Reference proteome; RNA-binding; Stress response; Transposition;
KW Zinc.
FT CHAIN 1..408
FT /note="RNA-guided DNA endonuclease TnpB"
FT /id="PRO_0000455634"
FT ACT_SITE 191
FT /evidence="ECO:0000305|PubMed:34619744"
FT ACT_SITE 278
FT /evidence="ECO:0000305|PubMed:34619744"
FT ACT_SITE 361
FT /evidence="ECO:0000305|PubMed:34619744"
FT BINDING 331
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:23461641"
FT BINDING 334
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:23461641"
FT BINDING 351
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:23461641"
FT BINDING 354
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:23461641"
FT MUTAGEN 191
FT /note="D->A: No longer cleaves dsDNA."
FT /evidence="ECO:0000269|PubMed:34619744"
FT MUTAGEN 331..334
FT /note="CHDC->SHDS: No longer inhibits ISDra2
FT transposition."
FT /evidence="ECO:0000269|PubMed:23461641"
FT MUTAGEN 351..354
FT /note="CPNC->SPNS: No longer inhibits ISDra2
FT transposition."
FT /evidence="ECO:0000269|PubMed:23461641"
SQ SEQUENCE 408 AA; 46400 MW; FA48BD28AC1521C5 CRC64;
MIRNKAFVVR LYPNAAQTEL INRTLGSARF VYNHFLARRI AAYKESGKGL TYGQTSSELT
LLKQAEETSW LSEVDKFALQ NSLKNLETAY KNFFRTVKQS GKKVGFPRFR KKRTGESYRT
QFTNNNIQIG EGRLKLPKLG WVKTKGQQDI QGKILNVTVR RIHEGHYEAS VLCEVEIPYL
PAAPKFAAGV DVGIKDFAIV TDGVRFKHEQ NPKYYRSTLK RLRKAQQTLS RRKKGSARYG
KAKTKLARIH KRIVNKRQDF LHKLTTSLVR EYEIIGTEHL KPDNMRKNRR LALSISDAGW
GEFIRQLEYK AAWYGRLVSK VSPYFPSSQL CHDCGFKNPE VKNLAVRTWT CPNCGETHDR
DENAALNIRR EALVAAGISD TLNAHGGYVR PASAGNGLRS ENHATLVV
