ID TOP1_ECOLI Reviewed; 865 AA. AC P06612; DT 01-JAN-1988, integrated into UniProtKB/Swiss-Prot. DT 01-FEB-1995, sequence version 2. DT 01-OCT-2014, entry version 156. DE RecName: Full=DNA topoisomerase 1 {ECO:0000255|HAMAP-Rule:MF_00952}; DE EC=5.99.1.2 {ECO:0000255|HAMAP-Rule:MF_00952}; DE AltName: Full=DNA topoisomerase I {ECO:0000255|HAMAP-Rule:MF_00952}; DE AltName: Full=Omega-protein; DE AltName: Full=Relaxing enzyme; DE AltName: Full=Swivelase; DE AltName: Full=Untwisting enzyme; GN Name=topA {ECO:0000255|HAMAP-Rule:MF_00952}; Synonyms=supX; GN OrderedLocusNames=b1274, JW1266; OS Escherichia coli (strain K12). OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; OC Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX PubMed=3029379; DOI=10.1016/0022-2836(86)90129-4; RA Tse-Dinh Y.-C., Wang J.C.; RT "Complete nucleotide sequence of the topA gene encoding Escherichia RT coli DNA topoisomerase I."; RL J. Mol. Biol. 191:321-331(1986). RN [2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND SEQUENCE REVISION. RA Lynch D.A., Wang J.C.; RL Submitted (SEP-1991) to the EMBL/GenBank/DDBJ databases. RN [3] 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., RA Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., RA Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., RA Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., RA Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.; RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome RT corresponding to the 28.0-40.1 min region on the linkage map."; RL DNA Res. 3:363-377(1996). RN [4] 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., RA Mau B., Shao Y.; RT "The complete genome sequence of Escherichia coli K-12."; RL Science 277:1453-1462(1997). RN [5] 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 RT MG1655 and W3110."; RL Mol. Syst. Biol. 2:E1-E5(2006). RN [6] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 698-865. RX PubMed=3032952; RA Ostrowski J., Jagura-Burdzy G., Kredich N.M.; RT "DNA sequences of the cysB regions of Salmonella typhimurium and RT Escherichia coli."; RL J. Biol. Chem. 262:5999-6005(1987). RN [7] RP IDENTIFICATION BY 2D-GEL. RX PubMed=9298644; DOI=10.1002/elps.1150180805; RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., RA Neidhardt F.C.; RT "Escherichia coli proteome analysis using the gene-protein database."; RL Electrophoresis 18:1243-1251(1997). RN [8] RP MUTAGENESIS OF GLU-9; TYR-319; ARG-321; HIS-365 AND THR-496, CATALYTIC RP ACTIVITY, FUNCTION, AND ACTIVE SITE. RX PubMed=9497321; DOI=10.1074/jbc.273.11.6050; RA Chen S.J., Wang J.C.; RT "Identification of active site residues in Escherichia coli DNA RT topoisomerase I."; RL J. Biol. Chem. 273:6050-6056(1998). RN [9] RP MUTAGENESIS OF ASP-111; ASP-113 AND GLU-115, COFACTOR, FUNCTION, RP ENZYME MECHANISM, METAL-BINDING SITES, AND CATALYTIC ACTIVITY. RX PubMed=10681504; DOI=10.1074/jbc.275.8.5318; RA Zhu C.X., Tse-Dinh Y.C.; RT "The acidic triad conserved in type IA DNA topoisomerases is required RT for binding of Mg(II) and subsequent conformational change."; RL J. Biol. Chem. 275:5318-5322(2000). RN [10] RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-597, PUTATIVE METAL-BINDING RP SITES, AND ACTIVE SITE. RX PubMed=8114910; DOI=10.1038/367138a0; RA Lima C.D., Wang J.C., Mondragon A.; RT "Three-dimensional structure of the 67K N-terminal fragment of E. coli RT DNA topoisomerase I."; RL Nature 367:138-146(1994). RN [11] RP STRUCTURE BY NMR OF 745-865. RX PubMed=7779808; DOI=10.1021/bi00023a008; RA Yu L., Zhu C.-X., Tse-Dinh Y.-C., Fesik S.W.; RT "Solution structure of the C-terminal single-stranded DNA-binding RT domain of Escherichia coli topoisomerase I."; RL Biochemistry 34:7622-7628(1995). RN [12] RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 214-477. RX PubMed=10504724; DOI=10.1038/13283; RA Feinberg H., Lima C.D., Mondragon A.; RT "Conformational changes in E. coli DNA topoisomerase I."; RL Nat. Struct. Biol. 6:918-922(1999). RN [13] RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 1-597 IN COMPLEXES WITH RP NUCLEOTIDES. RX PubMed=10504732; DOI=10.1038/13333; RA Feinberg H., Changela A., Mondragon A.; RT "Protein-nucleotide interactions in E. coli DNA topoisomerase I."; RL Nat. Struct. Biol. 6:961-968(1999). RN [14] RP X-RAY CRYSTALLOGRAPHY (1.67 ANGSTROMS) OF 1-592 OF MUTANT ARG-365 IN RP COMPLEX WITH SINGLE-STANDED DNA, MUTAGENESIS OF HIS-365, AND CATALYTIC RP ACTIVITY. RX PubMed=14604525; DOI=10.1016/j.str.2003.09.013; RA Perry K., Mondragon A.; RT "Structure of a complex between E. coli DNA topoisomerase I and RT single-stranded DNA."; RL Structure 11:1349-1358(2003). RN [15] RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-596 OF MUTANT ASN-111 IN RP COMPLEX WITH DNA, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, COFACTOR, RP MUTAGENESIS OF ARG-168 AND ASP-172, DNA-BINDING SITES, AND ENZYME RP MECHANISM. RX PubMed=21482796; DOI=10.1073/pnas.1100300108; RA Zhang Z., Cheng B., Tse-Dinh Y.C.; RT "Crystal structure of a covalent intermediate in DNA cleavage and RT rejoining by Escherichia coli DNA topoisomerase I."; RL Proc. Natl. Acad. Sci. U.S.A. 108:6939-6944(2011). CC -!- FUNCTION: Releases the supercoiling and torsional tension of DNA, CC which is introduced during the DNA replication and transcription, CC by transiently cleaving and rejoining one strand of the DNA CC duplex. Introduces a single-strand break via transesterification CC at a target site in duplex DNA. The scissile phosphodiester is CC attacked by the catalytic tyrosine of the enzyme, resulting in the CC formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the CC expulsion of a 3'-OH DNA strand. The free DNA strand then CC undergoes passage around the unbroken strand, thus removing DNA CC supercoils. Finally, in the religation step, the DNA 3'-OH attacks CC the covalent intermediate to expel the active-site tyrosine and CC restore the DNA phosphodiester backbone. {ECO:0000255|HAMAP- CC Rule:MF_00952, ECO:0000269|PubMed:10681504, CC ECO:0000269|PubMed:21482796, ECO:0000269|PubMed:9497321}. CC -!- CATALYTIC ACTIVITY: ATP-independent breakage of single-stranded CC DNA, followed by passage and rejoining. {ECO:0000255|HAMAP- CC Rule:MF_00952, ECO:0000269|PubMed:10681504, CC ECO:0000269|PubMed:14604525, ECO:0000269|PubMed:21482796, CC ECO:0000269|PubMed:9497321}. CC -!- COFACTOR: Magnesium. Binds two Mg(2+) ions per subunit. The CC magnesium ions form salt bridges with both the protein and the CC DNA. Can also accept other divalent metal cations, such as Mn(2+) CC and Ca(2+). {ECO:0000269|PubMed:10681504, CC ECO:0000269|PubMed:21482796}. CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00952, CC ECO:0000269|PubMed:14604525, ECO:0000269|PubMed:21482796}. CC -!- SIMILARITY: Belongs to the type IA topoisomerase family. CC {ECO:0000255|HAMAP-Rule:MF_00952}. CC -!- SIMILARITY: Contains 1 Toprim domain. {ECO:0000255|HAMAP- CC Rule:MF_00952}. 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; X04475; CAA28164.1; -; Genomic_DNA. DR EMBL; M15041; AAA23641.1; -; Genomic_DNA. DR EMBL; U00096; AAC74356.1; -; Genomic_DNA. DR EMBL; AP009048; BAA14811.1; -; Genomic_DNA. DR PIR; E64875; ISECTP. DR RefSeq; NP_415790.1; NC_000913.3. DR RefSeq; YP_489542.1; NC_007779.1. DR PDB; 1CY0; X-ray; 2.45 A; A=1-597. DR PDB; 1CY1; X-ray; 2.30 A; A=1-597. DR PDB; 1CY2; X-ray; 2.30 A; A=1-597. DR PDB; 1CY4; X-ray; 2.55 A; A=1-597. DR PDB; 1CY6; X-ray; 2.50 A; A=1-597. DR PDB; 1CY7; X-ray; 2.40 A; A=1-597. DR PDB; 1CY8; X-ray; 2.45 A; A=1-597. DR PDB; 1CY9; X-ray; 1.80 A; A/B=214-477. DR PDB; 1CYY; X-ray; 2.15 A; A/B=214-477. DR PDB; 1ECL; X-ray; 1.90 A; A=1-597. DR PDB; 1MW8; X-ray; 1.90 A; X=1-592. DR PDB; 1MW9; X-ray; 1.67 A; X=1-592. DR PDB; 1YUA; NMR; -; A=745-865. DR PDB; 3PWT; X-ray; 1.90 A; A=1-596. DR PDB; 3PX7; X-ray; 2.30 A; A=1-595. DR PDBsum; 1CY0; -. DR PDBsum; 1CY1; -. DR PDBsum; 1CY2; -. DR PDBsum; 1CY4; -. DR PDBsum; 1CY6; -. DR PDBsum; 1CY7; -. DR PDBsum; 1CY8; -. DR PDBsum; 1CY9; -. DR PDBsum; 1CYY; -. DR PDBsum; 1ECL; -. DR PDBsum; 1MW8; -. DR PDBsum; 1MW9; -. DR PDBsum; 1YUA; -. DR PDBsum; 3PWT; -. DR PDBsum; 3PX7; -. DR ProteinModelPortal; P06612; -. DR SMR; P06612; 2-619, 745-865. DR DIP; DIP-11011N; -. DR IntAct; P06612; 68. DR MINT; MINT-1218330; -. DR STRING; 511145.b1274; -. DR PaxDb; P06612; -. DR PRIDE; P06612; -. DR EnsemblBacteria; AAC74356; AAC74356; b1274. DR EnsemblBacteria; BAA14811; BAA14811; BAA14811. DR GeneID; 12930585; -. DR GeneID; 945862; -. DR KEGG; ecj:Y75_p1248; -. DR KEGG; eco:b1274; -. DR PATRIC; 32117806; VBIEscCol129921_1323. DR EchoBASE; EB1006; -. DR EcoGene; EG11013; topA. DR eggNOG; COG0551; -. DR HOGENOM; HOG000004018; -. DR KO; K03168; -. DR OMA; VVECDKC; -. DR OrthoDB; EOG6S7XQ9; -. DR PhylomeDB; P06612; -. DR BioCyc; EcoCyc:EG11013-MONOMER; -. DR BioCyc; ECOL316407:JW1266-MONOMER; -. DR BioCyc; MetaCyc:EG11013-MONOMER; -. DR EvolutionaryTrace; P06612; -. DR PRO; PR:P06612; -. DR Genevestigator; P06612; -. DR GO; GO:0005694; C:chromosome; IEA:InterPro. DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW. DR GO; GO:0003916; F:DNA topoisomerase activity; IMP:EcoCyc. DR GO; GO:0003917; F:DNA topoisomerase type I activity; IMP:EcoCyc. DR GO; GO:0003918; F:DNA topoisomerase type II (ATP-hydrolyzing) activity; IEA:InterPro. DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-HAMAP. DR GO; GO:0022616; P:DNA strand elongation; IMP:EcoCyc. DR GO; GO:0006265; P:DNA topological change; IGI:EcoliWiki. DR Gene3D; 1.10.460.10; -; 3. DR Gene3D; 2.70.20.10; -; 2. DR Gene3D; 3.40.50.140; -; 1. DR HAMAP; MF_00952; Topoisom_1_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; IPR023405; Topo_IA_core_domain. DR InterPro; IPR003602; Topo_IA_DNA-bd. DR InterPro; IPR013498; Topo_IA_Znf. DR InterPro; IPR005733; TopoI_bac-type. DR InterPro; IPR013263; TopoI_Znr_bac. DR InterPro; IPR028612; Topoisom_1_IA. DR InterPro; IPR006171; Toprim_domain. DR PANTHER; PTHR11390; PTHR11390; 1. DR Pfam; PF08272; Topo_Zn_Ribbon; 2. DR Pfam; PF01131; Topoisom_bac; 1. DR Pfam; PF01751; Toprim; 1. DR Pfam; PF01396; zf-C4_Topoisom; 2. 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; TIGR01051; topA_bact; 1. DR PROSITE; PS00396; TOPOISOMERASE_I_PROK; 1. DR PROSITE; PS50880; TOPRIM; 1. PE 1: Evidence at protein level; KW 3D-structure; Complete proteome; DNA-binding; Isomerase; Magnesium; KW Metal-binding; Reference proteome; Repeat; Topoisomerase; Zinc; KW Zinc-finger. FT CHAIN 1 865 DNA topoisomerase 1. FT /FTId=PRO_0000145147. FT DOMAIN 3 142 Toprim. {ECO:0000255|HAMAP- FT Rule:MF_00952}. FT ZN_FING 599 630 C4-type 1. FT ZN_FING 662 689 C4-type 2. FT ZN_FING 711 736 C4-type 3. FT REGION 192 197 Interaction with DNA. FT ACT_SITE 319 319 O-(5'-phospho-DNA)-tyrosine intermediate. FT {ECO:0000255|HAMAP-Rule:MF_00952, FT ECO:0000269|PubMed:21482796, FT ECO:0000269|PubMed:8114910, FT ECO:0000269|PubMed:9497321}. FT METAL 9 9 Magnesium 1; catalytic. FT {ECO:0000255|HAMAP-Rule:MF_00952}. FT METAL 111 111 Magnesium 1; catalytic. {ECO:0000305}. FT METAL 111 111 Magnesium 2. {ECO:0000305}. FT METAL 113 113 Magnesium 2. {ECO:0000305}. FT SITE 33 33 Interaction with DNA. FT SITE 168 168 Interaction with DNA. FT SITE 169 169 Interaction with DNA. FT SITE 172 172 Interaction with DNA. FT SITE 177 177 Interaction with DNA. FT SITE 184 184 Interaction with DNA. FT SITE 321 321 Interaction with DNA. FT SITE 507 507 Interaction with DNA. FT MUTAGEN 9 9 E->A: Abolishes enzyme activity. FT {ECO:0000269|PubMed:9497321}. FT MUTAGEN 9 9 E->Q: No effect on DNA cleavage activity. FT {ECO:0000269|PubMed:9497321}. FT MUTAGEN 111 111 D->A: Abolishes both magnesium binding FT and enzyme activity; when associated with FT A-113 and A-115. FT {ECO:0000269|PubMed:10681504}. FT MUTAGEN 113 113 D->A: Abolishes both magnesium binding FT and enzyme activity; when associated with FT A-111 and A-115. FT {ECO:0000269|PubMed:10681504}. FT MUTAGEN 115 115 E->A: Abolishes both magnesium binding FT and enzyme activity; when associated with FT A-111 and A-113. FT {ECO:0000269|PubMed:10681504}. FT MUTAGEN 168 168 R->A: Abolishes enzyme activity. FT {ECO:0000269|PubMed:21482796}. FT MUTAGEN 172 172 D->A: Abolishes enzyme activity. FT {ECO:0000269|PubMed:21482796}. FT MUTAGEN 319 319 Y->A: Abolishes enzyme activity. FT {ECO:0000269|PubMed:9497321}. FT MUTAGEN 321 321 R->A: Abolishes enzyme activity. FT {ECO:0000269|PubMed:9497321}. FT MUTAGEN 321 321 R->K: No effect. FT {ECO:0000269|PubMed:9497321}. FT MUTAGEN 365 365 H->A: No effect. FT {ECO:0000269|PubMed:14604525, FT ECO:0000269|PubMed:9497321}. FT MUTAGEN 365 365 H->R: Increases DNA binding affinity. FT {ECO:0000269|PubMed:14604525, FT ECO:0000269|PubMed:9497321}. FT MUTAGEN 496 496 T->A: No effect. FT {ECO:0000269|PubMed:9497321}. FT CONFLICT 787 787 P -> R (in Ref. 6; AAA23641). FT {ECO:0000305}. FT STRAND 4 9 FT HELIX 11 18 FT STRAND 25 29 FT STRAND 35 37 FT HELIX 64 71 FT STRAND 72 74 FT TURN 75 79 FT TURN 87 89 FT HELIX 90 101 FT STRAND 104 108 FT HELIX 114 127 FT HELIX 131 133 FT STRAND 134 136 FT HELIX 144 152 FT HELIX 159 186 FT HELIX 197 213 FT STRAND 218 227 FT STRAND 229 231 FT STRAND 233 241 FT HELIX 251 263 FT STRAND 266 278 FT HELIX 286 297 FT HELIX 301 313 FT STRAND 316 318 FT HELIX 329 342 FT HELIX 345 347 FT STRAND 356 358 FT STRAND 362 364 FT HELIX 377 379 FT HELIX 385 401 FT STRAND 406 417 FT STRAND 420 431 FT HELIX 433 437 FT STRAND 458 470 FT HELIX 479 488 FT TURN 494 496 FT HELIX 497 506 FT STRAND 509 513 FT STRAND 516 519 FT HELIX 521 533 FT HELIX 535 538 FT HELIX 540 554 FT HELIX 560 579 FT HELIX 582 584 FT STRAND 755 762 FT STRAND 764 767 FT STRAND 769 773 FT STRAND 776 778 FT STRAND 780 783 FT TURN 784 787 FT HELIX 797 802 FT TURN 803 806 FT HELIX 812 816 FT STRAND 827 832 FT TURN 833 836 FT STRAND 837 842 FT STRAND 853 855 SQ SEQUENCE 865 AA; 97350 MW; 8C13F767FE5B178C CRC64; MGKALVIVES PAKAKTINKY LGSDYVVKSS VGHIRDLPTS GSAAKKSADS TSTKTAKKPK KDERGALVNR MGVDPWHNWE AHYEVLPGKE KVVSELKQLA EKADHIYLAT DLDREGEAIA WHLREVIGGD DARYSRVVFN EITKNAIRQA FNKPGELNID RVNAQQARRF MDRVVGYMVS PLLWKKIARG LSAGRVQSVA VRLVVERERE IKAFVPEEFW EVDASTTTPS GEALALQVTH QNDKPFRPVN KEQTQAAVSL LEKARYSVLE REDKPTTSKP GAPFITSTLQ QAASTRLGFG VKKTMMMAQR LYEAGYITYM RTDSTNLSQD AVNMVRGYIS DNFGKKYLPE SPNQYASKEN SQEAHEAIRP SDVNVMAESL KDMEADAQKL YQLIWRQFVA CQMTPAKYDS TTLTVGAGDF RLKARGRILR FDGWTKVMPA LRKGDEDRIL PAVNKGDALT LVELTPAQHF TKPPARFSEA SLVKELEKRG IGRPSTYASI ISTIQDRGYV RVENRRFYAE KMGEIVTDRL EENFRELMNY DFTAQMENSL DQVANHEAEW KAVLDHFFSD FTQQLDKAEK DPEEGGMRPN QMVLTSIDCP TCGRKMGIRT ASTGVFLGCS GYALPPKERC KTTINLVPEN EVLNVLEGED AETNALRAKR RCPKCGTAMD SYLIDPKRKL HVCGNNPTCD GYEIEEGEFR IKGYDGPIVE CEKCGSEMHL KMGRFGKYMA CTNEECKNTR KILRNGEVAP PKEDPVPLPE LPCEKSDAYF VLRDGAAGVF LAANTFPKSR ETRAPLVEEL YRFRDRLPEK LRYLADAPQQ DPEGNKTMVR FSRKTKQQYV SSEKDGKATG WSAFYVDGKW VEGKK //