TOP3_ECOLI
ID TOP3_ECOLI Reviewed; 653 AA.
AC P14294;
DT 01-JAN-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1990, sequence version 1.
DT 03-AUG-2022, entry version 183.
DE RecName: Full=DNA topoisomerase 3 {ECO:0000255|HAMAP-Rule:MF_00953};
DE EC=5.6.2.1 {ECO:0000255|HAMAP-Rule:MF_00953, ECO:0000269|PubMed:6326814};
DE AltName: Full=DNA topoisomerase III {ECO:0000255|HAMAP-Rule:MF_00953};
GN Name=topB {ECO:0000255|HAMAP-Rule:MF_00953};
GN OrderedLocusNames=b1763, JW1752;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-20, AND FUNCTION.
RC STRAIN=HMS-83;
RX PubMed=2553698; DOI=10.1016/s0021-9258(19)84661-6;
RA Digate R.J., Marians K.J.;
RT "Molecular cloning and DNA sequence analysis of Escherichia coli topB, the
RT gene encoding topoisomerase III.";
RL J. Biol. Chem. 264:17924-17930(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP CATALYTIC ACTIVITY, FUNCTION, AND COFACTOR.
RX PubMed=6326814; DOI=10.1021/bi00304a002;
RA Srivenugopal K.S., Lockshon D., Morris D.R.;
RT "Escherichia coli DNA topoisomerase III: purification and characterization
RT of a new type I enzyme.";
RL Biochemistry 23:1899-1906(1984).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS), AND ACTIVE SITE.
RX PubMed=10574789; DOI=10.1016/s0969-2126(00)80027-1;
RA Mondragon A., DiGate R.;
RT "The structure of Escherichia coli DNA topoisomerase III.";
RL Structure 7:1373-1383(1999).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF MUTANT PHE-328 IN COMPLEX WITH
RP DNA.
RX PubMed=11429611; DOI=10.1038/35082615;
RA Changela A., DiGate R.J., Mondragon A.;
RT "Crystal structure of a complex of a type IA DNA topoisomerase with a
RT single-stranded DNA molecule.";
RL Nature 411:1077-1081(2001).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEXES WITH DNA.
RX PubMed=17331537; DOI=10.1016/j.jmb.2007.01.065;
RA Changela A., DiGate R.J., Mondragon A.;
RT "Structural studies of E. coli topoisomerase III-DNA complexes reveal a
RT novel type IA topoisomerase-DNA conformational intermediate.";
RL J. Mol. Biol. 368:105-118(2007).
CC -!- FUNCTION: Releases the supercoiling and torsional tension of DNA, which
CC is introduced during the DNA replication and transcription, by
CC transiently cleaving and rejoining one strand of the DNA duplex.
CC Introduces a single-strand break via transesterification at a target
CC site in duplex DNA. The scissile phosphodiester is attacked by the
CC catalytic tyrosine of the enzyme, resulting in the formation of a DNA-
CC (5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH
CC DNA strand. The free DNA strand then undergoes passage around the
CC unbroken strand, thus removing DNA supercoils. Finally, in the
CC religation step, the DNA 3'-OH attacks the covalent intermediate to
CC expel the active-site tyrosine and restore the DNA phosphodiester
CC backbone. TOP3 is a potent decatenase. {ECO:0000255|HAMAP-
CC Rule:MF_00953, ECO:0000269|PubMed:2553698, ECO:0000269|PubMed:6326814}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-independent breakage of single-stranded DNA, followed by
CC passage and rejoining.; EC=5.6.2.1; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00953, ECO:0000269|PubMed:6326814};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00953,
CC ECO:0000269|PubMed:6326814};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00953,
CC ECO:0000269|PubMed:6326814};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00953,
CC ECO:0000269|PubMed:6326814};
CC Note=Binds two Mg(2+) ions per subunit. The magnesium ions form salt
CC bridges with both the protein and the DNA. Can also accept other
CC divalent metal cations, such as Mn(2+) or Ca(2+). {ECO:0000255|HAMAP-
CC Rule:MF_00953, ECO:0000269|PubMed:6326814};
CC -!- INTERACTION:
CC P14294; P45544: frlR; NbExp=2; IntAct=EBI-552080, EBI-562481;
CC P14294; P28632: holD; NbExp=3; IntAct=EBI-552080, EBI-549176;
CC P14294; P21893: recJ; NbExp=4; IntAct=EBI-552080, EBI-556893;
CC -!- SIMILARITY: Belongs to the type IA topoisomerase family.
CC {ECO:0000255|HAMAP-Rule:MF_00953}.
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DR EMBL; J05076; AAA83923.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74833.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA15551.1; -; Genomic_DNA.
DR PIR; JV0049; JV0049.
DR RefSeq; NP_416277.1; NC_000913.3.
DR RefSeq; WP_001235800.1; NZ_SSZK01000001.1.
DR PDB; 1D6M; X-ray; 3.00 A; A=1-653.
DR PDB; 1I7D; X-ray; 2.05 A; A=1-653.
DR PDB; 2O19; X-ray; 2.45 A; A/B=1-653.
DR PDB; 2O54; X-ray; 2.50 A; A/B=1-653.
DR PDB; 2O59; X-ray; 2.50 A; A/B=1-653.
DR PDB; 2O5C; X-ray; 2.35 A; A/B=1-653.
DR PDB; 2O5E; X-ray; 2.50 A; A/B=1-653.
DR PDBsum; 1D6M; -.
DR PDBsum; 1I7D; -.
DR PDBsum; 2O19; -.
DR PDBsum; 2O54; -.
DR PDBsum; 2O59; -.
DR PDBsum; 2O5C; -.
DR PDBsum; 2O5E; -.
DR AlphaFoldDB; P14294; -.
DR SMR; P14294; -.
DR BioGRID; 4259137; 67.
DR BioGRID; 850501; 2.
DR DIP; DIP-11012N; -.
DR IntAct; P14294; 40.
DR STRING; 511145.b1763; -.
DR jPOST; P14294; -.
DR PaxDb; P14294; -.
DR PRIDE; P14294; -.
DR EnsemblBacteria; AAC74833; AAC74833; b1763.
DR EnsemblBacteria; BAA15551; BAA15551; BAA15551.
DR GeneID; 66674342; -.
DR GeneID; 946141; -.
DR KEGG; ecj:JW1752; -.
DR KEGG; eco:b1763; -.
DR PATRIC; fig|1411691.4.peg.491; -.
DR EchoBASE; EB1007; -.
DR eggNOG; COG0550; Bacteria.
DR HOGENOM; CLU_002929_5_2_6; -.
DR InParanoid; P14294; -.
DR OMA; TYPRVDT; -.
DR PhylomeDB; P14294; -.
DR BioCyc; EcoCyc:EG11014-MON; -.
DR BioCyc; MetaCyc:EG11014-MON; -.
DR BRENDA; 5.6.2.1; 2026.
DR EvolutionaryTrace; P14294; -.
DR PRO; PR:P14294; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0043597; C:cytoplasmic replication fork; IDA:EcoCyc.
DR GO; GO:0003917; F:DNA topoisomerase type I (single strand cut, ATP-independent) activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0098847; F:sequence-specific single stranded DNA binding; IDA:EcoCyc.
DR GO; GO:0051304; P:chromosome separation; IMP:EcoliWiki.
DR GO; GO:0006310; P:DNA recombination; IMP:EcoliWiki.
DR GO; GO:0006265; P:DNA topological change; IDA:EcoCyc.
DR GO; GO:0006261; P:DNA-templated DNA replication; IDA:EcoCyc.
DR CDD; cd00186; TOP1Ac; 1.
DR CDD; cd03362; TOPRIM_TopoIA_TopoIII; 1.
DR Gene3D; 1.10.290.10; -; 1.
DR Gene3D; 1.10.460.10; -; 1.
DR Gene3D; 2.70.20.10; -; 1.
DR HAMAP; MF_00953; Topoisom_3_prok; 1.
DR InterPro; IPR000380; Topo_IA.
DR InterPro; IPR003601; Topo_IA_2.
DR InterPro; IPR023406; Topo_IA_AS.
DR InterPro; IPR013497; Topo_IA_cen.
DR InterPro; IPR013824; Topo_IA_cen_sub1.
DR InterPro; IPR013825; Topo_IA_cen_sub2.
DR InterPro; IPR013826; Topo_IA_cen_sub3.
DR InterPro; IPR023405; Topo_IA_core_domain.
DR InterPro; IPR003602; Topo_IA_DNA-bd_dom.
DR InterPro; IPR005738; TopoIII.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034144; TOPRIM_TopoIII.
DR PANTHER; PTHR11390; PTHR11390; 1.
DR Pfam; PF01131; Topoisom_bac; 1.
DR Pfam; PF01751; Toprim; 1.
DR PRINTS; PR00417; PRTPISMRASEI.
DR SMART; SM00437; TOP1Ac; 1.
DR SMART; SM00436; TOP1Bc; 1.
DR SMART; SM00493; TOPRIM; 1.
DR SUPFAM; SSF56712; SSF56712; 1.
DR TIGRFAMs; TIGR01056; topB; 1.
DR PROSITE; PS00396; TOPOISOMERASE_I_PROK; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; DNA-binding; Isomerase; Magnesium;
KW Metal-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..653
FT /note="DNA topoisomerase 3"
FT /id="PRO_0000145184"
FT DOMAIN 1..134
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953"
FT REGION 194..199
FT /note="Interaction with DNA"
FT REGION 616..653
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 328
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953,
FT ECO:0000269|PubMed:10574789"
FT BINDING 7
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953"
FT BINDING 103
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953"
FT BINDING 103
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953"
FT BINDING 105
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00953"
FT SITE 61
FT /note="Interaction with DNA"
FT SITE 170
FT /note="Interaction with DNA"
FT SITE 178
FT /note="Interaction with DNA"
FT SITE 185
FT /note="Interaction with DNA"
FT SITE 330
FT /note="Interaction with DNA"
FT STRAND 2..8
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 9..16
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 24..26
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 29..32
FT /evidence="ECO:0007829|PDB:1I7D"
FT TURN 33..35
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 36..40
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 45..48
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 51..54
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 56..59
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 63..65
FT /evidence="ECO:0007829|PDB:2O19"
FT STRAND 75..77
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 79..81
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 82..94
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 96..101
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 106..118
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 123..127
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 129..131
FT /evidence="ECO:0007829|PDB:2O59"
FT HELIX 139..146
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 152..155
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 156..185
FT /evidence="ECO:0007829|PDB:1I7D"
FT TURN 186..188
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 199..214
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 220..229
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 235..240
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 244..246
FT /evidence="ECO:0007829|PDB:1I7D"
FT TURN 247..249
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 252..254
FT /evidence="ECO:0007829|PDB:2O59"
FT HELIX 259..269
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 278..286
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 294..305
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 309..321
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 338..343
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 344..354
FT /evidence="ECO:0007829|PDB:1I7D"
FT TURN 356..358
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 371..373
FT /evidence="ECO:0007829|PDB:1D6M"
FT HELIX 375..377
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 397..412
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 418..427
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 434..436
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 438..443
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 445..449
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 454..456
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 472..484
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 493..501
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 503..506
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 510..518
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 521..523
FT /evidence="ECO:0007829|PDB:1I7D"
FT TURN 525..527
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 528..537
FT /evidence="ECO:0007829|PDB:1I7D"
FT STRAND 540..550
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 552..560
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 563..566
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 569..582
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 588..607
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 612..614
FT /evidence="ECO:0007829|PDB:1I7D"
FT HELIX 649..653
FT /evidence="ECO:0007829|PDB:2O5C"
SQ SEQUENCE 653 AA; 73217 MW; 301566E14DDDD8C7 CRC64;
MRLFIAEKPS LARAIADVLP KPHRKGDGFI ECGNGQVVTW CIGHLLEQAQ PDAYDSRYAR
WNLADLPIVP EKWQLQPRPS VTKQLNVIKR FLHEASEIVH AGDPDREGQL LVDEVLDYLQ
LAPEKRQQVQ RCLINDLNPQ AVERAIDRLR SNSEFVPLCV SALARARADW LYGINMTRAY
TILGRNAGYQ GVLSVGRVQT PVLGLVVRRD EEIENFVAKD FFEVKAHIVT PADERFTAIW
QPSEACEPYQ DEEGRLLHRP LAEHVVNRIS GQPAIVTSYN DKRESESAPL PFSLSALQIE
AAKRFGLSAQ NVLDICQKLY ETHKLITYPR SDCRYLPEEH FAGRHAVMNA ISVHAPDLLP
QPVVDPDIRN RCWDDKKVDA HHAIIPTARS SAINLTENEA KVYNLIARQY LMQFCPDAVF
RKCVIELDIA KGKFVAKARF LAEAGWRTLL GSKERDEEND GTPLPVVAKG DELLCEKGEV
VERQTQPPRH FTDATLLSAM TGIARFVQDK DLKKILRATD GLGTEATRAG IIELLFKRGF
LTKKGRYIHS TDAGKALFHS LPEMATRPDM TAHWESVLTQ ISEKQCRYQD FMQPLVGTLY
QLIDQAKRTP VRQFRGIVAP GSGGSADKKK AAPRKRSAKK SPPADEVGSG AIA
