ID   TOP1_ALKPO              Reviewed;         707 AA.
AC   P34184; D3G1M5; D3G1M6;
DT   01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT   11-JAN-2011, sequence version 3.
DT   24-JAN-2024, entry version 133.
DE   RecName: Full=DNA topoisomerase 1;
DE            EC=5.6.2.1 {ECO:0000255|PROSITE-ProRule:PRU10131};
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; OrderedLocusNames=BpOF4_21279/BpOF4_21284;
OS   Alkalihalophilus pseudofirmus (strain ATCC BAA-2126 / JCM 17055 / OF4)
OS   (Bacillus pseudofirmus).
OG   Plasmid pBpOF4-01.
OC   Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Alkalihalophilus.
OX   NCBI_TaxID=398511;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-2126 / JCM 17055 / OF4; PLASMID=pBpOF4-01;
RX   PubMed=21951522; DOI=10.1111/j.1462-2920.2011.02591.x;
RA   Janto B., Ahmed A., Ito M., Liu J., Hicks D.B., Pagni S., Fackelmayer O.J.,
RA   Smith T.A., Earl J., Elbourne L.D., Hassan K., Paulsen I.T., Kolsto A.B.,
RA   Tourasse N.J., Ehrlich G.D., Boissy R., Ivey D.M., Li G., Xue Y., Ma Y.,
RA   Hu F.Z., Krulwich T.A.;
RT   "Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that
RT   support the ability to grow in an external pH range from 7.5 to 11.4.";
RL   Environ. Microbiol. 13:3289-3309(2011).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 27-706.
RX   PubMed=1329032; DOI=10.1093/nar/20.18.4928;
RA   Ivey D.M., Cheng J., Krulwich T.A.;
RT   "A 1.6 kb region of Bacillus firmus OF4 DNA encodes a homolog of
RT   Escherichia coli and yeast DNA topoisomerases and may contain a
RT   translational readthrough of UGA.";
RL   Nucleic Acids Res. 20:4928-4928(1992).
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 (By similarity). {ECO:0000250}.
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|PROSITE-
CC         ProRule:PRU10131};
CC   -!- SUBUNIT: Monomer. {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the type IA topoisomerase family.
CC       {ECO:0000255|PROSITE-ProRule:PRU01383, ECO:0000305}.
CC   -!- CAUTION: The sequence displayed is the result of a readthrough of the
CC       terminator UGA between codons for Tyr-288 and Leu-290. However,
CC       translational readthrough of UGA in this protein has not been proven.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=ADC52251.1; Type=Miscellaneous discrepancy; Note=Probable readthrough of the stop codon.; Evidence={ECO:0000305};
CC       Sequence=ADC52252.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC       Sequence=CAA78484.1; Type=Miscellaneous discrepancy; Note=Probable readthrough of the stop codon.; Evidence={ECO:0000305};
CC       Sequence=CAA78485.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC       Sequence=CAA78485.1; Type=Frameshift; Evidence={ECO:0000305};
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DR   EMBL; CP001879; ADC52251.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP001879; ADC52252.1; ALT_INIT; Genomic_DNA.
DR   EMBL; Z14112; CAA78484.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; Z14112; CAA78485.1; ALT_SEQ; Genomic_DNA.
DR   PIR; S23866; S23866.
DR   KEGG; bpf:BpOF4_21279; -.
DR   KEGG; bpf:BpOF4_21284; -.
DR   eggNOG; COG0550; Bacteria.
DR   HOGENOM; CLU_002929_5_0_9; -.
DR   Proteomes; UP000001544; Plasmid pBpOF4-01.
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-EC.
DR   GO; GO:0006265; P:DNA topological change; IEA:InterPro.
DR   CDD; cd03362; TOPRIM_TopoIA_TopoIII; 1.
DR   Gene3D; 3.40.50.140; -; 1.
DR   Gene3D; 3.30.65.10; Bacterial Topoisomerase I, domain 1; 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   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; IPR025589; Toprim_C_rpt.
DR   InterPro; IPR006171; TOPRIM_domain.
DR   InterPro; IPR034144; TOPRIM_TopoIII.
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   Pfam; PF13342; Toprim_Crpt; 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   SUPFAM; SSF57783; Zinc beta-ribbon; 1.
DR   PROSITE; PS00396; TOPO_IA_1; 1.
DR   PROSITE; PS52039; TOPO_IA_2; 1.
DR   PROSITE; PS50880; TOPRIM; 1.
PE   3: Inferred from homology;
KW   DNA-binding; Isomerase; Plasmid; Reference proteome;
KW   RNA suppression of termination; Topoisomerase.
FT   CHAIN           1..706
FT                   /note="DNA topoisomerase 1"
FT                   /id="PRO_0000145140"
FT   DOMAIN          1..140
FT                   /note="Toprim"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   DOMAIN          157..596
FT                   /note="Topo IA-type catalytic"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01383"
FT   REGION          199..204
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        323
FT                   /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01383"
FT   SITE            48
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   SITE            167
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   SITE            171
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   SITE            325
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   SITE            529
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT   CONFLICT        126
FT                   /note="Q -> H (in Ref. 2; CAA78484)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        142
FT                   /note="T -> F (in Ref. 2; CAA78484)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        218
FT                   /note="I -> L (in Ref. 2; CAA78484)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        254
FT                   /note="K -> T (in Ref. 2; CAA78484)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        258
FT                   /note="A -> D (in Ref. 2; CAA78484)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        352
FT                   /note="F -> S (in Ref. 2; CAA78485)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        443
FT                   /note="W -> R (in Ref. 2; CAA78485)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        523..524
FT                   /note="IT -> TH (in Ref. 2; CAA78485)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        548
FT                   /note="V -> A (in Ref. 2; CAA78485)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   707 AA;  80296 MW;  1E07919E5AD9AA00 CRC64;
     MYAILAEKPS AAKAYAQALN GKRQGRIYVA PPSSLLPEGA LICAAVGHIL EFLEPGELNE
     KYKSYSLDSL PIIIDLFQYK VVSDKKEVLQ RIKDTIFDKR VKTIILATDA AAEGEYIGRN
     ILYRLQCKKT IKRLWTSSMT ATSIQKAFSQ LKADAETLPL YYQAKARAES DYMIGLTLSR
     AYGILLKEQG IVPHNTTISL GRVQTPLLAE IVKRERLIEQ FTAENFWTVK ATFNNQGNVY
     EGEWFHEKEN RIFKEEQAEQ LCELVRNQSS TIMEMKEEMR TYQPPLLYXL STLQMDAGNA
     FGFKPAETLK YAQSLYDKGY LSYPRTQDER ITESDARELE NNIQFLSGHD TFGALFPLPV
     STLMNNKRYI GEVTDHHALL ITDKIPKDKD LSEDEKSIYH LVVKRILAAH YPDVAMSHKE
     IITKVMDRFT FRSKGKELLS KGWHHIIPPT NENDIMLPTL LKGSEGVVTD TLTTKSKTKP
     PNRYTSSSLI GFMKNAAQAI EDEDRKSISN LPLGTEATRA GLITLLESRK YIEWKKNKVY
     PTLLGITVVD SIKRGSVIKS PILTAKWDVK LNEIGASLYN HKDFIAHSKK LSSVLFEEVK
     TYSSTWNQNG VERIKSESIG ACLLCGSNVV LRKGKHGEFY GCSNYKDSGC TFNLPFKVLN
     KKLSKKQLME LLKNEKTDII KGFKWKDKTF NAPLVWNRED QKVQFGK
//