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-MAY-2013, entry version 144.
DE RecName: Full=DNA topoisomerase 1;
DE EC=5.99.1.2;
DE AltName: Full=DNA topoisomerase I;
DE AltName: Full=Omega-protein;
DE AltName: Full=Relaxing enzyme;
DE AltName: Full=Swivelase;
DE AltName: Full=Untwisting enzyme;
GN Name=topA; Synonyms=supX; 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 277:1453-1474(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.
CC -!- CATALYTIC ACTIVITY: ATP-independent breakage of single-stranded
CC DNA, followed by passage and rejoining.
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+).
CC -!- SUBUNIT: Monomer.
CC -!- SIMILARITY: Belongs to the type IA topoisomerase family.
CC -!- SIMILARITY: Contains 1 Toprim domain.
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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_000913.2.
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=1-596.
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; 65.
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; EFWDIHA; -.
DR ProtClustDB; PRK07561; -.
DR BioCyc; EcoCyc:EG11013-MONOMER; -.
DR BioCyc; ECOL316407:JW1266-MONOMER; -.
DR BioCyc; MetaCyc:EG11013-MONOMER; -.
DR EvolutionaryTrace; P06612; -.
DR Genevestigator; P06612; -.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
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:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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 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; 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; Topo_IA_core; 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; ATP-binding; Complete proteome; DNA-binding; Isomerase;
KW Magnesium; Metal-binding; Nucleotide-binding; Reference proteome;
KW Repeat; Topoisomerase; Zinc; Zinc-finger.
FT CHAIN 1 865 DNA topoisomerase 1.
FT /FTId=PRO_0000145147.
FT DOMAIN 3 142 Toprim.
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 METAL 9 9 Magnesium 1; catalytic (By similarity).
FT METAL 111 111 Magnesium 1; catalytic (Probable).
FT METAL 111 111 Magnesium 2 (Probable).
FT METAL 113 113 Magnesium 2 (Probable).
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 MUTAGEN 9 9 E->Q: No effect on DNA cleavage activity.
FT MUTAGEN 111 111 D->A: Abolishes both magnesium binding
FT and enzyme activity; when associated with
FT A-113 and A-115.
FT MUTAGEN 113 113 D->A: Abolishes both magnesium binding
FT and enzyme activity; when associated with
FT A-111 and A-115.
FT MUTAGEN 115 115 E->A: Abolishes both magnesium binding
FT and enzyme activity; when associated with
FT A-111 and A-113.
FT MUTAGEN 168 168 R->A: Abolishes enzyme activity.
FT MUTAGEN 172 172 D->A: Abolishes enzyme activity.
FT MUTAGEN 319 319 Y->A: Abolishes enzyme activity.
FT MUTAGEN 321 321 R->A: Abolishes enzyme activity.
FT MUTAGEN 321 321 R->K: No effect.
FT MUTAGEN 365 365 H->A: No effect.
FT MUTAGEN 365 365 H->R: Increases DNA binding affinity.
FT MUTAGEN 496 496 T->A: No effect.
FT CONFLICT 787 787 P -> R (in Ref. 6; AAA23641).
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
//
