TOP1_THEMA
ID TOP1_THEMA Reviewed; 633 AA.
AC P46799;
DT 01-NOV-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1995, sequence version 1.
DT 03-AUG-2022, entry version 159.
DE RecName: Full=DNA topoisomerase 1 {ECO:0000255|HAMAP-Rule:MF_00952};
DE EC=5.6.2.1 {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}; OrderedLocusNames=TM_0258;
OS Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826
OS / MSB8).
OC Bacteria; Thermotogae; Thermotogales; Thermotogaceae; Thermotoga.
OX NCBI_TaxID=243274;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=8547314; DOI=10.1016/0167-4781(96)83596-2;
RA Bouthier de la Tour C., Kaltoum H., Portemer C., Confalonieri F., Huber R.,
RA Duguet M.;
RT "Cloning and sequencing of the gene coding for topoisomerase I from the
RT extremely thermophilic eubacterium, Thermotoga maritima.";
RL Biochim. Biophys. Acta 1264:279-283(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8;
RX PubMed=10360571; DOI=10.1038/20601;
RA Nelson K.E., Clayton R.A., Gill S.R., Gwinn M.L., Dodson R.J., Haft D.H.,
RA Hickey E.K., Peterson J.D., Nelson W.C., Ketchum K.A., McDonald L.A.,
RA Utterback T.R., Malek J.A., Linher K.D., Garrett M.M., Stewart A.M.,
RA Cotton M.D., Pratt M.S., Phillips C.A., Richardson D.L., Heidelberg J.F.,
RA Sutton G.G., Fleischmann R.D., Eisen J.A., White O., Salzberg S.L.,
RA Smith H.O., Venter J.C., Fraser C.M.;
RT "Evidence for lateral gene transfer between Archaea and Bacteria from
RT genome sequence of Thermotoga maritima.";
RL Nature 399:323-329(1999).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 3-633, AND DISULFIDE BOND.
RX PubMed=16600296; DOI=10.1016/j.jmb.2006.03.012;
RA Hansen G., Harrenga A., Wieland B., Schomburg D., Reinemer P.;
RT "Crystal structure of full length topoisomerase I from Thermotoga
RT maritima.";
RL J. Mol. Biol. 358:1328-1340(2006).
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. {ECO:0000255|HAMAP-Rule:MF_00952}.
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_00952};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00952};
CC Note=Binds two Mg(2+) per subunit. {ECO:0000255|HAMAP-Rule:MF_00952};
CC -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00952}.
CC -!- SIMILARITY: Belongs to the type IA topoisomerase family.
CC {ECO:0000255|HAMAP-Rule:MF_00952}.
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DR EMBL; U27841; AAA68949.1; -; Genomic_DNA.
DR EMBL; AE000512; AAD35346.1; -; Genomic_DNA.
DR PIR; S62737; S62737.
DR RefSeq; NP_228071.1; NC_000853.1.
DR RefSeq; WP_004082962.1; NZ_CP011107.1.
DR PDB; 2GAI; X-ray; 1.70 A; A/B=3-633.
DR PDB; 2GAJ; X-ray; 1.95 A; A/B=3-633.
DR PDBsum; 2GAI; -.
DR PDBsum; 2GAJ; -.
DR AlphaFoldDB; P46799; -.
DR SMR; P46799; -.
DR STRING; 243274.THEMA_03435; -.
DR PRIDE; P46799; -.
DR EnsemblBacteria; AAD35346; AAD35346; TM_0258.
DR KEGG; tma:TM0258; -.
DR eggNOG; COG0550; Bacteria.
DR InParanoid; P46799; -.
DR OMA; PECKYTR; -.
DR OrthoDB; 223233at2; -.
DR BRENDA; 5.6.2.1; 6331.
DR BRENDA; 5.99.1.2; 6331.
DR EvolutionaryTrace; P46799; -.
DR Proteomes; UP000008183; Chromosome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003917; F:DNA topoisomerase type I (single strand cut, ATP-independent) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR CDD; cd00186; TOP1Ac; 1.
DR CDD; cd03363; TOPRIM_TopoIA_TopoI; 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_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; IPR013826; Topo_IA_cen_sub3.
DR InterPro; IPR023405; Topo_IA_core_domain.
DR InterPro; IPR003602; Topo_IA_DNA-bd_dom.
DR InterPro; IPR005733; TopoI_bac-type.
DR InterPro; IPR028612; Topoisom_1_IA.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034149; TOPRIM_TopoI.
DR PANTHER; PTHR42785; PTHR42785; 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; 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; Disulfide bond; DNA-binding; Isomerase; Magnesium;
KW Metal-binding; Reference proteome; Topoisomerase; Zinc; Zinc-finger.
FT CHAIN 1..633
FT /note="DNA topoisomerase 1"
FT /id="PRO_0000145169"
FT DOMAIN 6..115
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT ZN_FING 559..580
FT /note="C4-type"
FT REGION 164..169
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT REGION 601..633
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 601..624
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 288
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT BINDING 12
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_00952"
FT BINDING 84
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_00952"
FT BINDING 84
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT BINDING 86
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 36
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 140
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 141
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 144
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 149
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 156
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 290
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 475
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT DISULFID 559..578
FT /evidence="ECO:0000269|PubMed:16600296"
FT DISULFID 561..580
FT /evidence="ECO:0000269|PubMed:16600296"
FT STRAND 8..12
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 14..24
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 25..27
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 28..32
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 37..40
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 51..55
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 64..76
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 79..81
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 87..99
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 116..124
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 131..159
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 166..185
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 190..198
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 201..205
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 215..222
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 227..239
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 247..258
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 262..274
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 279..283
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 298..311
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 314..316
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 346..349
FT /evidence="ECO:0007829|PDB:2GAI"
FT TURN 350..352
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 355..371
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 376..386
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 393..403
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 405..408
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 431..438
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 447..456
FT /evidence="ECO:0007829|PDB:2GAI"
FT TURN 462..464
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 465..474
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 477..481
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 484..488
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 489..501
FT /evidence="ECO:0007829|PDB:2GAI"
FT TURN 503..506
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 508..522
FT /evidence="ECO:0007829|PDB:2GAI"
FT HELIX 528..540
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 553..558
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 560..562
FT /evidence="ECO:0007829|PDB:2GAJ"
FT STRAND 564..570
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 573..577
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 579..581
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 593..595
FT /evidence="ECO:0007829|PDB:2GAI"
FT STRAND 598..600
FT /evidence="ECO:0007829|PDB:2GAI"
SQ SEQUENCE 633 AA; 72695 MW; F7262A044060CFE9 CRC64;
MSKKVKKYIV VESPAKAKTI KSILGNEYEV FASMGHIIDL PKSKFGVDLE KDFEPEFAVI
KGKEKVVEKL KDLAKKGELL IASDMDREGE AIAWHIARVT NTLGRKNRIV FSEITPRVIR
EAVKNPREID MKKVRAQLAR RILDRIVGYS LSPVLWRNFK SNLSAGRVQS ATLKLVCDRE
REILRFVPKK YHRITVNFDG LTAEIDVKEK KFFDAETLKE IQSIDELVVE EKKVSVKKFA
PPEPFKTSTL QQEAYSKLGF SVSKTMMIAQ QLYEGVETKD GHIAFITYMR TDSTRVSDYA
KEEARNLITE VFGEEYVGSK RERRKSNAKI QDAHEAIRPT NVFMTPEEAG KYLNSDQKKL
YELIWKRFLA SQMKPSQYEE TRFVLRTKDG KYRFKGTVLK KIFDGYEKVW KTERNTGEFP
FEEGESVKPV VVKIEEQETK PKPRYTEGSL VKEMERLGIG RPSTYASTIK LLLNRGYIKK
IRGYLYPTIV GSVVMDYLEK KYSDVVSVSF TAEMEKDLDE VEQGKKTDKI VLREFYESFS
SVFDRNDRIV VDFPTNQKCS CGKEMRLSFG KYGFYLKCEC GKTRSVKNDE IAVIDDGKIF
LGRKDSESGS PDGRSVEGKG NLSEKRRKGK KGS
