ID D2NRA3_ROTMD Unreviewed; 928 AA.
AC D2NRA3;
DT 02-MAR-2010, integrated into UniProtKB/TrEMBL.
DT 02-MAR-2010, sequence version 1.
DT 27-MAR-2024, entry version 89.
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=RMDY18_03470 {ECO:0000313|EMBL:BAI64179.1};
OS Rothia mucilaginosa (strain DY-18) (Stomatococcus mucilaginosus).
OC Bacteria; Actinomycetota; Actinomycetes; Micrococcales; Micrococcaceae;
OC Rothia.
OX NCBI_TaxID=680646 {ECO:0000313|EMBL:BAI64179.1, ECO:0000313|Proteomes:UP000001883};
RN [1] {ECO:0000313|Proteomes:UP000001883}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DY-18 {ECO:0000313|Proteomes:UP000001883};
RA Yamane K., Nambu T., Mashimo C., Sugimori C., Yamanaka T., Leung K.,
RA Fukushima H.;
RT "Complete genome sequence of Rothia mucilaginosa DJ.";
RL Submitted (JUL-2009) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:BAI64179.1, ECO:0000313|Proteomes:UP000001883}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DY-18 {ECO:0000313|EMBL:BAI64179.1,
RC ECO:0000313|Proteomes:UP000001883};
RA Yamane K., Yoshida M., Fujihira T., Baba T., Tsuji N., Hayashi H.,
RA Sugimori C., Yamanaka T., Mashimo C., Nambu T., Kawai H., Fukushima H.;
RT "Isolation and identification of Rothia mucilaginosa from persistent apical
RT periodontitis lesions.";
RL J Osaka Dent Univ 44:93-98(2010).
RN [3] {ECO:0000313|EMBL:BAI64179.1, ECO:0000313|Proteomes:UP000001883}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DY-18 {ECO:0000313|EMBL:BAI64179.1,
RC ECO:0000313|Proteomes:UP000001883};
RA Yamane K., Nambu T., Yamanaka T., Mashimo C., Sugimori C., Leung K.-P.,
RA Fukushima H.;
RT "Complete Genome Sequence of Rothia mucilaginosa DY-18: A Clinical Isolate
RT with Dense Meshwork-Like Structures from a Persistent Apical Periodontitis
RT Lesion.";
RL Sequencing 2010:457236-457236(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}.
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DR EMBL; AP011540; BAI64179.1; -; Genomic_DNA.
DR RefSeq; WP_012902943.1; NC_013715.1.
DR AlphaFoldDB; D2NRA3; -.
DR STRING; 680646.RMDY18_03470; -.
DR KEGG; rmu:RMDY18_03470; -.
DR eggNOG; COG0550; Bacteria.
DR eggNOG; COG1754; Bacteria.
DR HOGENOM; CLU_002929_2_0_11; -.
DR Proteomes; UP000001883; 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; 3.40.50.140; -; 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; 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 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 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:UP000001883};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_00952}.
FT DOMAIN 9..132
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT REGION 181..186
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT REGION 726..748
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 889..928
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 896..920
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 325
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 39
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 158
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 161
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 166
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 173
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 327
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 530
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
SQ SEQUENCE 928 AA; 102060 MW; 772BCBD670909419 CRC64;
MPAQAKTGKA LLIVESPSKV KTISSYLGED YLVDSSMGHI RDLPQPSELP ENLKKSPVGK
FAVNVEENFE PYYVVNPDKK KKVAELKRKL KEVDALYLAT DGDREGEAIA WHLKEVLKPK
VPVYRMTFPE ITREAIQRAF GELRDIDLHL VDAQETRRIL DRIYGYEISP VLWRKVGRGL
SAGRVQSVAT RLVVERERER MAFVAANYWD LSGRFLTAAS EGFDAKLVAV DGNRIATGKD
FADNGTLNTS KVTHLNEEAA RALAAALQSA AFSVRSVETK PYKRRPAAPF TTSTLQQEAA
RKLRFSSRVT MQVAQRLYEN GYITYMRTDS VALSEQAISA ARRQASELYG AEFVPSAPRV
YTSKSKNAQE AHEAIRPAGD TFRTPDAVRG SLSNDEFRLY ELIWKRTVAS QMADATGSTA
SVRLGAVASN GQDAEFAASG TVITFRGFLA AYEEGVDASR VAEREAKDAE KRLPNLTTGE
ALTAEAIEPA GHETLPPPRY TEASLVKTLD ELGIGRPSTY AAVISTIMDR GYVNVRSGSL
IPSWIAFSVV RLLESSFGPY VNYEFTAQME EDLDRIARGE ESRVEWLGEF YFGGGSKRGL
KPIVDNLGEI DARSINSIPI ADGIVLRVGK FGPYLEAEGT LDTETGELTE PIRANVPADL
APDELTEEKA RELLEQGKSD GRVLGVDPVS GNQIVARDGR YGPYVTEVIE EMTEEQIQAY
LDAQPTEYYK NGKPKPKKKP KPAKPRTASL FKSMDLATVT LEQALQLMSL PRVLGTDAEG
VEITVQNGRF GPYLKKGTDS RSIGSEDEIF TITLEQALEI YSQPKQRGRA AAKPPLAELG
VDPVSEKKIV VKDGRFGPYI TDGITNITVP RAESVESLTH ERAVQLLADK RAKGPVKRKT
AAKKTTTAKK TTAKKTTTRK TAAKKTAE
//
