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Transposase for transposon Tn5 (EC 3.1.-.-) (Tnp)

 TN5P_ECOLX              Reviewed;         476 AA.
Q46731; Q08JA5; Q47661; Q57460;
14-OCT-2008, integrated into UniProtKB/Swiss-Prot.
01-NOV-1996, sequence version 1.
18-JUL-2018, entry version 86.
RecName: Full=Transposase for transposon Tn5;
EC=3.1.-.-;
AltName: Full=Tnp;
Name=tnpA; Synonyms=tnp;
Escherichia coli.
Plasmid pO86A1.
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=562;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS 1 AND 2), AND FUNCTION.
PubMed=6260374; DOI=10.1016/0092-8674(81)90284-1;
Rothstein S.J., Reznikoff W.S.;
"The functional differences in the inverted repeats of Tn5 are caused
by a single base pair nonhomology.";
Cell 23:191-199(1981).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS 1 AND 2).
PubMed=6271452;
Auerswald E.A., Ludwig G., Schaller H.;
"Structural analysis of Tn5.";
Cold Spring Harb. Symp. Quant. Biol. 45:107-113(1981).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1).
PubMed=7867940; DOI=10.1016/0378-1119(94)00854-L;
Ahmed A., Podemski L.;
"The revised nucleotide sequence of Tn5.";
Gene 154:129-130(1995).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORM 1).
STRAIN=DIJ1; PLASMID=pO86A1;
Yamamoto T.;
"pO86A1 is a Tn5-insert derivative of adherence plasmid pO86A in
strain DIJ1.";
Submitted (MAR-2006) to the EMBL/GenBank/DDBJ databases.
[5]
PROTEIN SEQUENCE OF N-TERMINUS, AND ALTERNATIVE PROMOTER USAGE.
PubMed=2438419; DOI=10.1016/0022-2836(86)90028-8;
Krebs M.P., Reznikoff W.S.;
"Transcriptional and translational initiation sites of IS50. Control
of transposase and inhibitor expression.";
J. Mol. Biol. 192:781-791(1986).
[6]
FUNCTION.
PubMed=6291786; DOI=10.1016/0092-8674(82)90292-6;
Johnson R.C., Yin J.C.P., Reznikoff W.S.;
"Control of Tn5 transposition in Escherichia coli is mediated by
protein from the right repeat.";
Cell 30:873-882(1982).
[7]
FUNCTION.
PubMed=6303899;
Lowe J.B., Berg D.E.;
"A product of the Tn5 transposase gene inhibits transposition.";
Genetics 103:605-615(1983).
[8]
FUNCTION, AND MUTAGENESIS OF MET-56; GLU-110 AND GLU-345.
PubMed=1310499; DOI=10.1128/jb.174.4.1229-1239.1992;
Wiegand T.W., Reznikoff W.S.;
"Characterization of two hypertransposing Tn5 mutants.";
J. Bacteriol. 174:1229-1239(1992).
[9]
FUNCTION, AND SUBUNIT.
PubMed=8226636;
de la Cruz N.B., Weinreich M.D., Wiegand T.W., Krebs M.P.,
Reznikoff W.S.;
"Characterization of the Tn5 transposase and inhibitor proteins: a
model for the inhibition of transposition.";
J. Bacteriol. 175:6932-6938(1993).
[10]
FUNCTION, AND SUBUNIT.
PubMed=8871560; DOI=10.1093/nar/24.19.3790;
York D., Reznikoff W.S.;
"Purification and biochemical analyses of a monomeric form of Tn5
transposase.";
Nucleic Acids Res. 24:3790-3796(1996).
[11]
MUTAGENESIS OF TYR-41; THR-47 AND GLU-54.
PubMed=9268665; DOI=10.1006/jmbi.1997.1188;
Zhou M., Reznikoff W.S.;
"Tn5 transposase mutants that alter DNA binding specificity.";
J. Mol. Biol. 271:362-373(1997).
[12]
MUTAGENESIS OF ARG-30; LYS-40 AND ARG-62.
PubMed=11283001; DOI=10.1074/jbc.M010748200;
Twining S.S., Goryshin I.Y., Bhasin A., Reznikoff W.S.;
"Functional characterization of arginine 30, lysine 40, and arginine
62 in Tn5 transposase.";
J. Biol. Chem. 276:23135-23143(2001).
[13]
FUNCTION, AND MUTAGENESIS OF ASP-97; ASP-188; TYR-319; ARG-322;
GLU-326; LYS-330 AND LYS-333.
PubMed=11877443; DOI=10.1074/jbc.M200742200;
Naumann T.A., Reznikoff W.S.;
"Tn5 transposase active site mutants.";
J. Biol. Chem. 277:17623-17629(2002).
[14]
MUTAGENESIS OF ARG-342; GLU-344; ASN-348; SER-438; LYS-439 AND
SER-445.
PubMed=17693501; DOI=10.1128/JB.00524-07;
Vaezeslami S., Sterling R., Reznikoff W.S.;
"Site-directed mutagenesis studies of Tn5 transposase residues
involved in synaptic complex formation.";
J. Bacteriol. 189:7436-7441(2007).
[15]
REVIEW.
PubMed=18680433; DOI=10.1146/annurev.genet.42.110807.091656;
Reznikoff W.S.;
"Transposon tn5.";
Annu. Rev. Genet. 42:269-286(2008).
[16]
X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) OF 56-476.
PubMed=10207011; DOI=10.1074/jbc.274.17.11904;
Davies D.R., Mahnke Braam L., Reznikoff W.S., Rayment I.;
"The three-dimensional structure of a Tn5 transposase-related protein
determined to 2.9-A resolution.";
J. Biol. Chem. 274:11904-11913(1999).
[17]
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF MUTANT LYS-54/ALA-56/PRO-372
IN COMPLEX WITH DNA AND MANGANESE IONS, COFACTOR, AND SUBUNIT.
PubMed=10884228; DOI=10.1126/science.289.5476.77;
Davies D.R., Goryshin I.Y., Reznikoff W.S., Rayment I.;
"Three-dimensional structure of the Tn5 synaptic complex transposition
intermediate.";
Science 289:77-85(2000).
[18]
X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF MUTANT
LYS-54/ALA-56/LYS-345/PRO-372 IN COMPLEX WITH DNA AND MANGANESE IONS,
AND FUNCTION.
PubMed=12367522; DOI=10.1016/S0022-2836(02)00877-X;
Steiniger-White M., Bhasin A., Lovell S., Rayment I., Reznikoff W.S.;
"Evidence for 'unseen' transposase-DNA contacts.";
J. Mol. Biol. 322:971-982(2002).
[19]
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF MUTANT
LYS-54/ALA-56/LYS-119/ALA-120/LYS-345/PRO-372 IN COMPLEX WITH
MANGANESE IONS AND DNA, COFACTOR, AND SUBUNIT.
PubMed=11896402; DOI=10.1038/nsb778;
Lovell S., Goryshin I.Y., Reznikoff W.R., Rayment I.;
"Two-metal active site binding of a Tn5 transposase synaptic
complex.";
Nat. Struct. Biol. 9:278-281(2002).
[20]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF MUTANT
LYS-54/ALA-56/LYS-119/ALA-120/LYS-345/PRO-372 IN COMPLEX WITH DNA AND
MANGANESE IONS, SUBUNIT, AND COFACTOR.
PubMed=15102449; DOI=10.1016/j.sbi.2004.01.008;
Steiniger-White M., Rayment I., Reznikoff W.S.;
"Structure/function insights into Tn5 transposition.";
Curr. Opin. Struct. Biol. 14:50-57(2004).
-!- FUNCTION: Mediates transposition of transposon Tn5 by a 'cut and
paste' mechanism. First, the monomeric transposase binds the 19 bp
inverted DNA repeats flanking the transposon. Then, dimerization
of the DNA-bound transposase creates a synaptic DNA complex. After
nicking of the first DNA strand, excision of the transposon
proceeds through a series of intermediates. The transposase then
mediates the insertion of the transposon at a new site by strand
transfer. The activity of the wild-type transposase is very low,
and is further inhibited by dimerization with the transposase
inhibitor (inh). {ECO:0000269|PubMed:11877443,
ECO:0000269|PubMed:12367522, ECO:0000269|PubMed:1310499,
ECO:0000269|PubMed:6260374, ECO:0000269|PubMed:6291786,
ECO:0000269|PubMed:6303899, ECO:0000269|PubMed:8226636,
ECO:0000269|PubMed:8871560}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:10884228,
ECO:0000269|PubMed:11896402, ECO:0000269|PubMed:15102449};
Note=Binds 2 magnesium ions per subunit.
{ECO:0000269|PubMed:10884228, ECO:0000269|PubMed:11896402,
ECO:0000269|PubMed:15102449};
-!- SUBUNIT: Monomer. Homodimer of tnp (isoform 1), and heterodimer of
tnp (isoform 1) and inh (isoform 2). {ECO:0000269|PubMed:10884228,
ECO:0000269|PubMed:11896402, ECO:0000269|PubMed:12367522,
ECO:0000269|PubMed:15102449, ECO:0000269|PubMed:8226636,
ECO:0000269|PubMed:8871560}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative promoter usage; Named isoforms=2;
Name=1; Synonyms=Transposase, Tnp;
IsoId=Q46731-1; Sequence=Displayed;
Name=2; Synonyms=Transposition inhibitor, Inh;
IsoId=Q46731-2; Sequence=VSP_035522;
Note=Expressed at 4 times higher levels than isoform 1.;
-!- MISCELLANEOUS: Tn5 is a bacterial transposon that contains three
genes conferring resistance to the antibiotics kanamycin/neomycin,
bleomycin and streptomycin, flanked by two IS50 elements. IS50R
codes for the functional transposase (isoform 1) and for the
transposition inhibitor (isoform 2). IS50L differs by one
nucleotide, giving rise to an ochre stop codon and producing C-
terminally truncated proteins that lack transposase activity.
-!- SIMILARITY: Belongs to the transposase 11 family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAF34032.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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EMBL; U00004; AAA73393.1; -; Genomic_DNA.
EMBL; U00004; AAA73394.1; -; Genomic_DNA.
EMBL; V00617; CAA23891.1; -; Genomic_DNA.
EMBL; U15573; AAB60064.1; -; Genomic_DNA.
EMBL; AB255435; BAF34032.1; ALT_INIT; Genomic_DNA.
RefSeq; WP_000633033.1; NZ_PGJZ01000120.1.
RefSeq; YP_788129.1; NC_008460.1.
PDB; 1B7E; X-ray; 2.90 A; A=56-476.
PDB; 1MM8; X-ray; 2.80 A; A=1-476.
PDB; 1MUH; X-ray; 2.30 A; A=1-476.
PDB; 1MUS; X-ray; 1.90 A; A=1-476.
PDB; 3ECP; X-ray; 2.50 A; A=1-476.
PDB; 4DM0; X-ray; 2.50 A; A=1-476.
PDBsum; 1B7E; -.
PDBsum; 1MM8; -.
PDBsum; 1MUH; -.
PDBsum; 1MUS; -.
PDBsum; 3ECP; -.
PDBsum; 4DM0; -.
ProteinModelPortal; Q46731; -.
SMR; Q46731; -.
DIP; DIP-17010N; -.
PRIDE; Q46731; -.
GeneID; 4364164; -.
EvolutionaryTrace; Q46731; -.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0004803; F:transposase activity; IEA:InterPro.
GO; GO:0006313; P:transposition, DNA-mediated; IEA:InterPro.
Gene3D; 1.10.246.40; -; 1.
Gene3D; 1.10.740.10; -; 1.
Gene3D; 3.90.350.10; -; 1.
InterPro; IPR012337; RNaseH-like_sf.
InterPro; IPR038215; TN5-like_N_sf.
InterPro; IPR002559; Transposase_11.
InterPro; IPR003201; Transposase_Tn5.
InterPro; IPR014737; Transposase_Tn5-like_C.
InterPro; IPR014736; Transposase_Tn5-like_core.
InterPro; IPR014735; Transposase_Tn5-like_N.
Pfam; PF01609; DDE_Tnp_1; 1.
Pfam; PF02281; Dimer_Tnp_Tn5; 1.
Pfam; PF14706; Tnp_DNA_bind; 1.
SUPFAM; SSF53098; SSF53098; 1.
1: Evidence at protein level;
3D-structure; Alternative promoter usage; Direct protein sequencing;
DNA recombination; DNA-binding; Endonuclease; Hydrolase; Magnesium;
Metal-binding; Nuclease; Plasmid; Transposable element; Transposition.
CHAIN 1 476 Transposase for transposon Tn5.
/FTId=PRO_0000351545.
REGION 1 70 Interaction with DNA.
REGION 237 255 Interaction with DNA.
REGION 319 348 Interaction with DNA.
REGION 369 476 Important for dimerization.
METAL 97 97 Magnesium 1.
METAL 97 97 Magnesium 2.
METAL 188 188 Magnesium 1.
METAL 326 326 Magnesium 2.
SITE 210 210 Interaction with DNA.
SITE 298 298 Interaction with DNA.
VAR_SEQ 1 55 Missing (in isoform 2). {ECO:0000305}.
/FTId=VSP_035522.
MUTAGEN 30 30 R->Q: Loss of transposase activity.
{ECO:0000269|PubMed:11283001}.
MUTAGEN 40 40 K->Q: Strongly reduced transposase
activity. {ECO:0000269|PubMed:11283001}.
MUTAGEN 41 41 Y->H: Enhances interaction with DNA and
increases transposition frequency.
{ECO:0000269|PubMed:9268665}.
MUTAGEN 47 47 T->P: Enhances interaction with DNA and
increases transposition frequency.
{ECO:0000269|PubMed:9268665}.
MUTAGEN 54 54 E->K,V: Enhances interaction with DNA and
increases transposition frequency.
{ECO:0000269|PubMed:9268665}.
MUTAGEN 56 56 M->A: Abolishes expression of the
transposase inhibitor Inh (isoform 2).
{ECO:0000269|PubMed:1310499}.
MUTAGEN 62 62 R->Q: Loss of transposase activity.
{ECO:0000269|PubMed:11283001}.
MUTAGEN 97 97 D->A: Loss of transposase activity.
{ECO:0000269|PubMed:11877443}.
MUTAGEN 110 110 E->K: Enhances transposase activity.
{ECO:0000269|PubMed:1310499}.
MUTAGEN 188 188 D->A: Loss of transposase activity.
{ECO:0000269|PubMed:11877443}.
MUTAGEN 319 319 Y->A: Loss of strand transfer activity.
{ECO:0000269|PubMed:11877443}.
MUTAGEN 322 322 R->A,K: Loss of strand transfer activity.
{ECO:0000269|PubMed:11877443}.
MUTAGEN 322 322 R->Q: Strongly reduced strand transfer
activity. {ECO:0000269|PubMed:11877443}.
MUTAGEN 326 326 E->A: Loss of transposase activity.
{ECO:0000269|PubMed:11877443}.
MUTAGEN 330 330 K->A: Reduced transposase activity.
{ECO:0000269|PubMed:11877443}.
MUTAGEN 330 330 K->R: No effect.
{ECO:0000269|PubMed:11877443}.
MUTAGEN 333 333 K->A,R: Strongly reduced DNA cleavage.
Loss of strand transfer activity.
{ECO:0000269|PubMed:11877443}.
MUTAGEN 342 342 R->A: Abolishes formation of the synaptic
complex and transposition.
{ECO:0000269|PubMed:17693501}.
MUTAGEN 344 344 E->A: Enhances transposase activity.
{ECO:0000269|PubMed:17693501}.
MUTAGEN 345 345 E->K: Enhances transposase activity.
{ECO:0000269|PubMed:1310499}.
MUTAGEN 348 348 N->A: Reduces formation of synaptic
complex and transposition.
{ECO:0000269|PubMed:17693501}.
MUTAGEN 372 372 L->P: Enhances transposase activity.
MUTAGEN 438 438 S->A: Abolishes formation of the synaptic
complex and transposition.
{ECO:0000269|PubMed:17693501}.
MUTAGEN 439 439 K->A: Abolishes formation of synaptic
complex and transposition.
{ECO:0000269|PubMed:17693501}.
MUTAGEN 445 445 S->A: Reduces formation of synaptic
complex and transposition.
{ECO:0000269|PubMed:17693501}.
MUTAGEN 462 462 G->D: Abolishes formation of the synaptic
complex and transposition.
MUTAGEN 466 466 A->D: Abolishes formation of the synaptic
complex and transposition.
CONFLICT 64 64 I -> Y (in Ref. 1; AAA73393/AAA73394 and
2; CAA23891). {ECO:0000305}.
CONFLICT 200 200 K -> R (in Ref. 1; AAA73393/AAA73394 and
2; CAA23891). {ECO:0000305}.
CONFLICT 225 225 Y -> I (in Ref. 1; AAA73393/AAA73394 and
2; CAA23891). {ECO:0000305}.
CONFLICT 303 303 S -> G (in Ref. 1; AAA73393/AAA73394 and
2; CAA23891). {ECO:0000305}.
STRAND 5 8 {ECO:0000244|PDB:3ECP}.
HELIX 9 17 {ECO:0000244|PDB:1MUS}.
STRAND 22 24 {ECO:0000244|PDB:3ECP}.
HELIX 25 40 {ECO:0000244|PDB:1MUS}.
TURN 41 43 {ECO:0000244|PDB:1MUS}.
HELIX 46 49 {ECO:0000244|PDB:1MUS}.
TURN 50 52 {ECO:0000244|PDB:1MUS}.
HELIX 54 64 {ECO:0000244|PDB:1MUS}.
HELIX 71 86 {ECO:0000244|PDB:1MUS}.
STRAND 92 103 {ECO:0000244|PDB:1MUS}.
HELIX 106 110 {ECO:0000244|PDB:1MUS}.
STRAND 114 116 {ECO:0000244|PDB:1MUS}.
STRAND 122 133 {ECO:0000244|PDB:1MUS}.
TURN 134 136 {ECO:0000244|PDB:1MUS}.
STRAND 139 148 {ECO:0000244|PDB:1MUS}.
HELIX 154 156 {ECO:0000244|PDB:1MUS}.
HELIX 161 163 {ECO:0000244|PDB:1MUS}.
HELIX 164 176 {ECO:0000244|PDB:1MUS}.
HELIX 177 182 {ECO:0000244|PDB:1MUS}.
STRAND 183 187 {ECO:0000244|PDB:1MUS}.
HELIX 189 191 {ECO:0000244|PDB:1MUS}.
HELIX 194 202 {ECO:0000244|PDB:1MUS}.
STRAND 206 210 {ECO:0000244|PDB:1MUS}.
TURN 218 220 {ECO:0000244|PDB:1MUS}.
HELIX 224 229 {ECO:0000244|PDB:1MUS}.
STRAND 235 241 {ECO:0000244|PDB:1MUS}.
STRAND 244 247 {ECO:0000244|PDB:1MUS}.
STRAND 253 256 {ECO:0000244|PDB:1MUS}.
STRAND 259 272 {ECO:0000244|PDB:1MUS}.
HELIX 274 276 {ECO:0000244|PDB:1MUS}.
STRAND 277 288 {ECO:0000244|PDB:1MUS}.
STRAND 291 293 {ECO:0000244|PDB:1MUS}.
STRAND 297 304 {ECO:0000244|PDB:1MUS}.
HELIX 309 320 {ECO:0000244|PDB:1MUS}.
HELIX 323 333 {ECO:0000244|PDB:1MUS}.
TURN 334 336 {ECO:0000244|PDB:1MUS}.
HELIX 338 340 {ECO:0000244|PDB:1MUS}.
HELIX 346 370 {ECO:0000244|PDB:1MUS}.
HELIX 382 388 {ECO:0000244|PDB:1B7E}.
HELIX 393 395 {ECO:0000244|PDB:1MUS}.
HELIX 399 409 {ECO:0000244|PDB:1MUS}.
TURN 410 412 {ECO:0000244|PDB:1MUS}.
STRAND 414 416 {ECO:0000244|PDB:1B7E}.
STRAND 419 421 {ECO:0000244|PDB:1MM8}.
HELIX 422 432 {ECO:0000244|PDB:1MUS}.
STRAND 438 440 {ECO:0000244|PDB:1B7E}.
HELIX 446 471 {ECO:0000244|PDB:1MUS}.
SEQUENCE 476 AA; 53306 MW; B52F2F143646AF10 CRC64;
MITSALHRAA DWAKSVFSSA ALGDPRRTAR LVNVAAQLAK YSGKSITISS EGSEAMQEGA
YRFIRNPNVS AEAIRKAGAM QTVKLAQEFP ELLAIEDTTS LSYRHQVAEE LGKLGSIQDK
SRGWWVHSVL LLEATTFRTV GLLHQEWWMR PDDPADADEK ESGKWLAAAA TSRLRMGSMM
SNVIAVCDRE ADIHAYLQDK LAHNERFVVR SKHPRKDVES GLYLYDHLKN QPELGGYQIS
IPQKGVVDKR GKRKNRPARK ASLSLRSGRI TLKQGNITLN AVLAEEINPP KGETPLKWLL
LTSEPVESLA QALRVIDIYT HRWRIEEFHK AWKTGAGAER QRMEEPDNLE RMVSILSFVA
VRLLQLRESF TLPQALRAQG LLKEAEHVES QSAETVLTPD ECQLLGYLDK GKRKRKEKAG
SLQWAYMAIA RLGGFMDSKR TGIASWGALW EGWEALQSKL DGFLAAKDLM AQGIKI


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