DRA2A_DEIRA
ID DRA2A_DEIRA Reviewed; 140 AA.
AC Q7DF83; O83028;
DT 25-MAY-2022, integrated into UniProtKB/Swiss-Prot.
DT 18-APR-2012, sequence version 1.
DT 03-AUG-2022, entry version 63.
DE RecName: Full=ISDra2 transposase TnpA {ECO:0000303|PubMed:20090938};
DE Short=TnpA-Dra2 {ECO:0000303|PubMed:20890269};
DE AltName: Full=Transposase for insertion sequence element IS200/IS605;
GN Name=tnpA {ECO:0000303|PubMed:20090938};
GN Synonyms=orf1 {ECO:0000303|PubMed:14676423},
GN tnpB {ECO:0000312|EMBL:BAA32389.1};
GN OrderedLocusNames=DR_0667 {ECO:0000312|EMBL:AAF10242.1};
GN and
GN OrderedLocusNames=DR_0979 {ECO:0000312|EMBL:AAF10556.1};
GN and
GN OrderedLocusNames=DR_1382 {ECO:0000312|EMBL:AAF10953.1};
GN and
GN OrderedLocusNames=DR_1592 {ECO:0000312|EMBL:AAF11155.1};
GN and
GN OrderedLocusNames=DR_1652 {ECO:0000312|EMBL:AAF11209.1};
GN and
GN OrderedLocusNames=DR_1932 {ECO:0000312|EMBL:AAF11485.1};
GN and
GN OrderedLocusNames=DR_2323 {ECO:0000312|EMBL:AAF11871.1};
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:BAA32389.1}
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:AAF10953.1}
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 IRRADIATION, 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 TRANSPOSITION INTO LAGGING STRAND.
RC STRAIN=R1 / ISDra2f;
RX PubMed=20691900; DOI=10.1016/j.cell.2010.06.034;
RA Ton-Hoang B., Pasternak C., Siguier P., Guynet C., Hickman A.B., Dyda F.,
RA Sommer S., Chandler M.;
RT "Single-stranded DNA transposition is coupled to host replication.";
RL Cell 142:398-408(2010).
RN [6]
RP FUNCTION, ACTIVITY REGULATION, AND DISRUPTION PHENOTYPE.
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 [7] {ECO:0007744|PDB:2XM3, ECO:0007744|PDB:2XMA, ECO:0007744|PDB:2XO6, ECO:0007744|PDB:2XQC}
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEX WITH MAGNESIUM AND DNA,
RP COFACTOR, SUBUNIT, DOMAIN, ACTIVE SITE, AND MUTAGENESIS OF ARG-14 AND
RP 122-SER-GLU-123.
RX PubMed=20890269; DOI=10.1038/emboj.2010.241;
RA Hickman A.B., James J.A., Barabas O., Pasternak C., Ton-Hoang B.,
RA Chandler M., Sommer S., Dyda F.;
RT "DNA recognition and the precleavage state during single-stranded DNA
RT transposition in D. radiodurans.";
RL EMBO J. 29:3840-3852(2010).
CC -!- FUNCTION: A transposase that is part of insertion sequence (IS) element
CC ISDra2, it is necessary and sufficient for both transposon excision and
CC insertion of ISDra2. This protein alone can be provided in trans and
CC allows transposition of an empty IS element (tnpA or tnpA-tnpB replaced
CC by a selectable marker) (PubMed:16359337, PubMed:20090938). ISDra2
CC binds subterminal imperfect palindromes at the left (LE) and right (RE)
CC ends of the element and cleaves only the 'top strand' which is
CC circularized and subsequently reinserted into the DNA target. This is
CC called a 'peel and paste' mechanism and increases the copy number of
CC the IS (Probable) (PubMed:20890269). Transposition is linked to DNA
CC replication in the absence of irradiation, with maximal activity when
CC the 'top strand' is on the replication lagging strand, and occurs
CC preferentially on the lagging strand (PubMed:20691900). The IS element
CC inserts 3' of the target sequence 5'-TTGAT-3'; target duplication has
CC not been observed (PubMed:14676423, PubMed:16359337, PubMed:20090938,
CC PubMed:20691900). {ECO:0000269|PubMed:14676423,
CC ECO:0000269|PubMed:16359337, ECO:0000269|PubMed:20090938,
CC ECO:0000269|PubMed:20691900, ECO:0000269|PubMed:20890269,
CC ECO:0000305|PubMed:20090938}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:20890269};
CC Note=Mg(2+), Mn(2+) and Cd(2+) support DNA cleavage whereas Ca(2+) and
CC Zn(2+) do not. {ECO:0000269|PubMed:20890269};
CC -!- ACTIVITY REGULATION: Both the excision and insertion steps are
CC inhibited by TnpB. {ECO:0000269|PubMed:23461641}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:20890269}.
CC -!- INDUCTION: Transposition of this element is induced approximately 100-
CC fold by 10 kGy gamma irradiation and approximately 50-fold by 600
CC J/m(2) of UV irradiation, both of which damage DNA. It rarely
CC transposes without irradiation (PubMed:16359337). Both excision and
CC insertion of ISDra2 are increased by irradiation, transposition occurs
CC in irradiated cells, probably triggered by single-stranded DNA formed
CC during genome reassembly, and is not due to specific induction of TnpA
CC expression (PubMed:20090938). {ECO:0000269|PubMed:16359337,
CC ECO:0000269|PubMed:20090938}.
CC -!- DOMAIN: The helix containing the catalytic Tyr-132 (residues 127-133)
CC is highly mobile. Recognition of the 5-base sequence immediately
CC preceding the cleavage site is mediated by base-pairing to an imperfect
CC palindrome, by sandwiching the fifth nucleotide between Tyr-30 and Trp-
CC 107 and hydrogen bonding to His-32, and by main chain atoms of Leu-106
CC and Trp-107. {ECO:0000269|PubMed:20890269}.
CC -!- DISRUPTION PHENOTYPE: When tested in an R1 strain with only a single
CC IS200 element (DR_1651 and DR_1652), required for transposition of the
CC IS element; single tnpA or double tnpA-tnpB deletions leads to loss of
CC transposition. {ECO:0000269|PubMed:20090938,
CC ECO:0000269|PubMed:23461641}.
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 -!- SIMILARITY: Belongs to the transposase 17 family. {ECO:0000305}.
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DR EMBL; AB016803; BAA32389.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF10242.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF10556.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF10953.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF11155.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF11209.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF11485.1; -; Genomic_DNA.
DR EMBL; AE000513; AAF11871.1; -; Genomic_DNA.
DR PIR; F75335; F75335.
DR RefSeq; NP_294390.1; NC_001263.1.
DR RefSeq; NP_294703.1; NC_001263.1.
DR RefSeq; NP_295105.1; NC_001263.1.
DR RefSeq; NP_295315.1; NC_001263.1.
DR RefSeq; NP_295375.1; NC_001263.1.
DR RefSeq; NP_295655.1; NC_001263.1.
DR RefSeq; NP_296044.1; NC_001263.1.
DR RefSeq; WP_010887312.1; NZ_CP015081.1.
DR PDB; 2XM3; X-ray; 2.30 A; A/B/C/D/E/F=1-140.
DR PDB; 2XMA; X-ray; 2.30 A; A/B/E/F=1-140.
DR PDB; 2XO6; X-ray; 1.90 A; A/D=1-140.
DR PDB; 2XQC; X-ray; 1.90 A; A/D=1-140.
DR PDBsum; 2XM3; -.
DR PDBsum; 2XMA; -.
DR PDBsum; 2XO6; -.
DR PDBsum; 2XQC; -.
DR SMR; Q7DF83; -.
DR STRING; 243230.DR_0667; -.
DR EnsemblBacteria; AAF10242; AAF10242; DR_0667.
DR EnsemblBacteria; AAF10556; AAF10556; DR_0979.
DR EnsemblBacteria; AAF10953; AAF10953; DR_1382.
DR EnsemblBacteria; AAF11155; AAF11155; DR_1592.
DR EnsemblBacteria; AAF11209; AAF11209; DR_1652.
DR EnsemblBacteria; AAF11485; AAF11485; DR_1932.
DR EnsemblBacteria; AAF11871; AAF11871; DR_2323.
DR KEGG; dra:DR_0667; -.
DR KEGG; dra:DR_0979; -.
DR KEGG; dra:DR_1382; -.
DR KEGG; dra:DR_1592; -.
DR KEGG; dra:DR_1652; -.
DR KEGG; dra:DR_1932; -.
DR KEGG; dra:DR_2323; -.
DR PATRIC; fig|243230.17.peg.1166; -.
DR eggNOG; COG1943; Bacteria.
DR HOGENOM; CLU_101320_2_0_0; -.
DR InParanoid; Q7DF83; -.
DR OMA; WNCKYHV; -.
DR OrthoDB; 1547701at2; -.
DR EvolutionaryTrace; Q7DF83; -.
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:0004803; F:transposase activity; IDA:UniProtKB.
DR GO; GO:0006313; P:transposition, DNA-mediated; IDA:UniProtKB.
DR Gene3D; 3.30.70.1290; -; 1.
DR InterPro; IPR002686; Transposase_17.
DR InterPro; IPR036515; Transposase_17_sf.
DR Pfam; PF01797; Y1_Tnp; 1.
DR SMART; SM01321; Y1_Tnp; 1.
DR SUPFAM; SSF143422; SSF143422; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA recombination; DNA-binding; Endonuclease; Hydrolase;
KW Magnesium; Metal-binding; Nuclease; Reference proteome; Stress response;
KW Transposable element; Transposition.
FT CHAIN 1..140
FT /note="ISDra2 transposase TnpA"
FT /id="PRO_0000455635"
FT REGION 127..133
FT /note="Mobile alpha helix"
FT /evidence="ECO:0000269|PubMed:20890269"
FT ACT_SITE 132
FT /note="Nucleophile"
FT /evidence="ECO:0000305|PubMed:20890269"
FT BINDING 67
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305|PubMed:20890269"
FT BINDING 69
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305|PubMed:20890269"
FT BINDING 136
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000305|PubMed:20890269"
FT SITE 14
FT /note="Critical for recognizing and stabilizing G:T
FT mismatch in DNA substrate"
FT /evidence="ECO:0000269|PubMed:20890269"
FT MUTAGEN 14
FT /note="R->A: 60-fold decrease in excision frequency, 30-
FT fold decrease in DNA binding."
FT /evidence="ECO:0000269|PubMed:20890269"
FT MUTAGEN 122..123
FT /note="SE->GG: 2-fold decrease in excision frequency."
FT /evidence="ECO:0000269|PubMed:20890269"
SQ SEQUENCE 140 AA; 16115 MW; BADD6C55185ECE0A CRC64;
MTYVILPLEM KKGRGYVYQL EYHLIWCVKY RHQVLVGEVA DGLKDILRDI AAQNGLEVIT
MEVMPDHVHL LLSATPQQAI PDFVKALKGA SARRMFVAYP QLKEKLWGGN LWNPSYCILT
VSENTRAQIQ KYIESQHDKE
