ID B2IEN4_BEII9 Unreviewed; 961 AA.
AC B2IEN4;
DT 10-JUN-2008, integrated into UniProtKB/TrEMBL.
DT 10-JUN-2008, sequence version 1.
DT 27-MAR-2024, entry version 104.
DE RecName: Full=DNA topoisomerase 1 {ECO:0000256|HAMAP-Rule:MF_00952};
DE EC=5.6.2.1 {ECO:0000256|HAMAP-Rule:MF_00952};
DE AltName: Full=DNA topoisomerase I {ECO:0000256|HAMAP-Rule:MF_00952};
GN Name=topA {ECO:0000256|HAMAP-Rule:MF_00952};
GN OrderedLocusNames=Bind_3417 {ECO:0000313|EMBL:ACB96974.1};
OS Beijerinckia indica subsp. indica (strain ATCC 9039 / DSM 1715 / NCIMB
OS 8712).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC Beijerinckiaceae; Beijerinckia.
OX NCBI_TaxID=395963 {ECO:0000313|EMBL:ACB96974.1, ECO:0000313|Proteomes:UP000001695};
RN [1] {ECO:0000313|Proteomes:UP000001695}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 9039 / DSM 1715 / NCIMB 8712
RC {ECO:0000313|Proteomes:UP000001695};
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., LaButti K., Schmutz J., Larimer F.,
RA Land M., Hauser L., Kyrpides N., Mikhailova N., Dunfield P.F., Dedysh S.N.,
RA Liesack W., Saw J.H., Alam M., Chen Y., Murrell J.C., Richardson P.;
RT "Complete sequence of chromosome of Beijerinckia indica subsp. indica ATCC
RT 9039.";
RL Submitted (MAR-2008) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:ACB96974.1, ECO:0000313|Proteomes:UP000001695}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 9039 / DSM 1715 / NCIMB 8712
RC {ECO:0000313|Proteomes:UP000001695};
RX PubMed=20601475; DOI=10.1128/JB.00656-10;
RA Tamas I., Dedysh S.N., Liesack W., Stott M.B., Alam M., Murrell J.C.,
RA Dunfield P.F.;
RT "Complete genome sequence of Beijerinckia indica subsp. indica.";
RL J. Bacteriol. 192:4532-4533(2010).
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:0000256|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;
CC Evidence={ECO:0000256|ARBA:ARBA00000213, ECO:0000256|HAMAP-
CC Rule:MF_00952};
CC -!- SUBUNIT: Monomer. {ECO:0000256|HAMAP-Rule:MF_00952}.
CC -!- SIMILARITY: Belongs to the type IA topoisomerase family.
CC {ECO:0000256|ARBA:ARBA00009446, ECO:0000256|HAMAP-Rule:MF_00952}.
CC -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC feature annotation. {ECO:0000256|HAMAP-Rule:MF_00952}.
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DR EMBL; CP001016; ACB96974.1; -; Genomic_DNA.
DR RefSeq; WP_012386322.1; NC_010581.1.
DR AlphaFoldDB; B2IEN4; -.
DR STRING; 395963.Bind_3417; -.
DR KEGG; bid:Bind_3417; -.
DR eggNOG; COG0550; Bacteria.
DR eggNOG; COG1754; Bacteria.
DR HOGENOM; CLU_002929_0_2_5; -.
DR OrthoDB; 9804262at2; -.
DR Proteomes; UP000001695; Chromosome.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
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; 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 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; IPR013498; Topo_IA_Znf.
DR InterPro; IPR005733; TopoI_bac-type.
DR InterPro; IPR028612; Topoisom_1_IA.
DR InterPro; IPR025589; Toprim_C_rpt.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034149; TOPRIM_TopoI.
DR NCBIfam; TIGR01051; topA_bact; 1.
DR PANTHER; PTHR42785:SF1; DNA TOPOISOMERASE; 1.
DR PANTHER; PTHR42785; DNA TOPOISOMERASE, TYPE IA, CORE; 1.
DR Pfam; PF01131; Topoisom_bac; 1.
DR Pfam; PF01751; Toprim; 1.
DR Pfam; PF13368; Toprim_C_rpt; 4.
DR Pfam; PF01396; zf-C4_Topoisom; 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; TOPOISOMERASE_I_PROK; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 3: Inferred from homology;
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|HAMAP-
KW Rule:MF_00952};
KW Isomerase {ECO:0000256|ARBA:ARBA00023235, ECO:0000256|HAMAP-Rule:MF_00952};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW Reference proteome {ECO:0000313|Proteomes:UP000001695};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_00952}; Zinc {ECO:0000256|ARBA:ARBA00022833};
KW Zinc-finger {ECO:0000256|ARBA:ARBA00022771}.
FT DOMAIN 1..117
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT REGION 165..170
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT REGION 904..961
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 303
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 31
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 141
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 142
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 145
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 157
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 305
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 500
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
SQ SEQUENCE 961 AA; 104697 MW; 1F104C40274B344F CRC64;
MNVVIVESPA KAKTINKYLG KDYEVFASFG HVRDLPPKDG SVDPDHDFAM LWDVDTKSAK
RLADIAKAVK EADRVILATD PDREGEAISW HVLEVLKAKK VLKDKPVERV VFNAITQSAI
LDAMRHPRAI DIDLVDAYLA RRALDYLVGF NLSPVLWRKL PGARSAGRVQ SVALRLVCER
ELEIERFVPR EYWSLTAFLR TPADQPFSAK LVGADGKKIN RLDIGAGAEA EAFKAALETA
KFTVAKVEAK PARRNPAPPF TTSTLQQEAA RKLGLAPART MQLAQRLYEG IDLDGETVGL
ITYMRTDGVD LAPEAITGAR KVIAAEYGDK YVPQAPRRYQ VKAKNAQEAH EAIRPTDLAR
LPKHVARFLD AEQARLYDLI WTRTIASQME SAELERTTVD ILAEVGARRL DLRATGQVVR
FDGFLKLYQE GRDDEEDEEG GRLPAMQVGD PLKKDRIEAS QHFTEPPPRF TEATLVKRME
ELGIGRPSTY ASTLAVLKDR EYVRIDKKRL IPEDKGRLVT AFLESFFGRY VGYDFTADLE
SSLDKISNHE IDWKQVLRDF WADFSGAIAD TKDLRTTQVL DSLNEVLGPY IFPDKGDGSN
PRACPSCANG QLSLKLGKFG SFIGCSNYPE CKFTRTLSDT GPEGGNGETD RPGVKVLGVD
AETGEEISLR DGRFGAYVQR GEGEKPKRAS LPKTIAPADL TLDMALGLLS LPREVARHPE
THEPILAGIG RFGPYVQHGK TYANIGKDED ILTLGANRAI DLIIAKESGL TGRRFGKGES
APARVLGDHP EGGQVTIKAG RFGPYVNYGK LNATLPKDAD PTTLTLEEGL ALLAAKASGQ
GGGKGAVQGQ LLGEHPSGGP ITVREGRFGP YVNHGKVNAT LKSGLSPETL TLEEAIRLID
EKAGAASKKA PAKKAPAKKA SGKTTTTEKA PAKKAASKAA TAKTTKAKAA KSSEPDEEPP
F
//
