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 04-NOV-2026, entry version 201. 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; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; OC Enterobacterales; 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, 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 OF MUTANT PHE-328 IN COMPLEX WITH 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 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; Evidence={ECO:0000255|HAMAP- CC Rule:MF_00953, ECO:0000269|PubMed:6326814}; CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000255|HAMAP- CC Rule:MF_00953, ECO:0000269|PubMed:6326814}; CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Evidence={ECO:0000255|HAMAP- CC Rule:MF_00953, 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, ECO:0000255|PROSITE- CC ProRule:PRU01383}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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_CP009789.1. DR PDB; 11FC; X-ray; 2.10 A; A=1-640. DR PDB; 11GX; X-ray; 2.22 A; A=1-640. DR PDB; 11KB; X-ray; 1.90 A; A=1-640. DR PDB; 11LB; X-ray; 1.85 A; A=1-640. DR PDB; 11YY; X-ray; 2.20 A; A=1-640. 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 AlphaFoldDB; P14294; -. DR SMR; P14294; -. DR BioGRID; 4259137; 70. DR BioGRID; 850501; 2. DR DIP; DIP-11012N; -. DR FunCoup; P14294; 177. DR IntAct; P14294; 40. DR STRING; 511145.b1763; -. DR jPOST; P14294; -. DR PaxDb; 511145-b1763; -. DR EnsemblBacteria; AAC74833; AAC74833; b1763. DR GeneID; 946141; -. DR KEGG; ecj:JW1752; -. DR KEGG; eco:b1763; -. DR KEGG; ecoc:C3026_10060; -. 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; AACEPYQ; -. DR OrthoDB; 9803554at2; -. DR PhylomeDB; P14294; -. DR BioCyc; EcoCyc:EG11014-MONOMER; -. DR BioCyc; MetaCyc:EG11014-MONOMER; -. DR BRENDA; 5.6.2.1; 2026. DR EvolutionaryTrace; P14294; -. DR PRO; PR:P14294; -. 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:0006281; P:DNA repair; IBA:GO_Central. 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 FunFam; 1.10.290.10:FF:000004; DNA topoisomerase 3; 1. DR FunFam; 1.10.460.10:FF:000004; DNA topoisomerase 3; 1. DR FunFam; 3.40.50.140:FF:000004; DNA topoisomerase 3; 1. DR Gene3D; 3.40.50.140; -; 1. DR Gene3D; 1.10.460.10; Topoisomerase I, domain 2; 1. DR Gene3D; 2.70.20.10; Topoisomerase I, domain 3; 1. DR Gene3D; 1.10.290.10; Topoisomerase I, domain 4; 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_dom. DR InterPro; IPR034144; TOPRIM_TopoIII. DR NCBIfam; NF005829; PRK07726.1; 1. DR NCBIfam; TIGR01056; topB; 1. DR PANTHER; PTHR11390:SF21; DNA TOPOISOMERASE 3-ALPHA; 1. DR PANTHER; PTHR11390; PROKARYOTIC DNA TOPOISOMERASE; 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; Prokaryotic type I DNA topoisomerase; 1. DR PROSITE; PS00396; TOPO_IA_1; 1. DR PROSITE; PS52039; TOPO_IA_2; 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 DOMAIN 155..603 FT /note="Topo IA-type catalytic" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01383" 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|PROSITE-ProRule:PRU01383, 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:11LB" FT HELIX 9..18 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 23..25 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 27..32 FT /evidence="ECO:0007829|PDB:11LB" FT TURN 33..35 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 36..40 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 45..48 FT /evidence="ECO:0007829|PDB:1I7D" FT HELIX 51..54 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 56..59 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 63..65 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 75..77 FT /evidence="ECO:0007829|PDB:1I7D" FT HELIX 79..92 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 96..101 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 106..118 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 123..126 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 128..131 FT /evidence="ECO:0007829|PDB:11YY" FT HELIX 139..147 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 152..154 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 159..186 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 199..214 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 220..229 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 235..241 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 244..249 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 252..254 FT /evidence="ECO:0007829|PDB:2O59" FT HELIX 259..269 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 273..286 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 287..291 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 294..305 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 309..317 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 318..322 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 338..343 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 344..354 FT /evidence="ECO:0007829|PDB:11LB" FT TURN 356..358 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 371..373 FT /evidence="ECO:0007829|PDB:1D6M" FT HELIX 375..377 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 397..412 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 418..429 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 432..443 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 445..449 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 453..455 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 456..458 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 462..465 FT /evidence="ECO:0007829|PDB:11KB" FT STRAND 472..484 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 487..490 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 493..501 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 503..506 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 510..518 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 521..523 FT /evidence="ECO:0007829|PDB:11LB" FT TURN 525..527 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 528..537 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 540..544 FT /evidence="ECO:0007829|PDB:11LB" FT STRAND 547..550 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 552..560 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 563..566 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 569..582 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 588..607 FT /evidence="ECO:0007829|PDB:11LB" FT HELIX 612..614 FT /evidence="ECO:0007829|PDB:11LB" 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 //