ID I3R2A8_HALMT Unreviewed; 855 AA.
AC I3R2A8;
DT 05-SEP-2012, integrated into UniProtKB/TrEMBL.
DT 05-SEP-2012, sequence version 1.
DT 27-MAR-2024, entry version 70.
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 ECO:0000313|EMBL:AFK18368.1};
GN OrderedLocusNames=HFX_0644 {ECO:0000313|EMBL:AFK18368.1};
GN ORFNames=BM92_06020 {ECO:0000313|EMBL:AHZ22236.1}, C439_07245
GN {ECO:0000313|EMBL:EMA02358.1}, E6P09_06265
GN {ECO:0000313|EMBL:QCQ74879.1};
OS Haloferax mediterranei (strain ATCC 33500 / DSM 1411 / JCM 8866 / NBRC
OS 14739 / NCIMB 2177 / R-4) (Halobacterium mediterranei).
OC Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Haloferacales;
OC Haloferacaceae; Haloferax.
OX NCBI_TaxID=523841 {ECO:0000313|EMBL:AFK18368.1, ECO:0000313|Proteomes:UP000006469};
RN [1] {ECO:0000313|EMBL:AFK18368.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=CGMCC 1.2087 {ECO:0000313|EMBL:AFK18368.1};
RX PubMed=22247127; DOI=10.1128/AEM.07114-11;
RA Cai S., Cai L., Liu H., Liu X., Han J., Zhou J., Xiang H.;
RT "Identification of the haloarchaeal phasin (PhaP) that functions in
RT polyhydroxyalkanoate accumulation and granule formation in Haloferax
RT mediterranei.";
RL Appl. Environ. Microbiol. 78:1946-1952(2012).
RN [2] {ECO:0000313|EMBL:AFK18368.1, ECO:0000313|Proteomes:UP000006469}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 /
RC R-4 {ECO:0000313|Proteomes:UP000006469}, and CGMCC 1.2087
RC {ECO:0000313|EMBL:AFK18368.1};
RX PubMed=22843593; DOI=10.1128/JB.00880-12;
RA Han J., Zhang F., Hou J., Liu X., Li M., Liu H., Cai L., Zhang B., Chen Y.,
RA Zhou J., Hu S., Xiang H.;
RT "Complete genome sequence of the metabolically versatile halophilic
RT archaeon Haloferax mediterranei, a poly(3-hydroxybutyrate-co-3-
RT hydroxyvalerate) producer.";
RL J. Bacteriol. 194:4463-4464(2012).
RN [3] {ECO:0000313|Proteomes:UP000011603}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33500 / DSM 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 /
RC R-4 {ECO:0000313|Proteomes:UP000011603};
RA Becker E.A., Seitzer P., Tritt A., Larsen D., Yao A., Wu D., Darling A.,
RA Eisen J.A., Facciotti M.T.;
RL Submitted (NOV-2012) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000313|EMBL:EMA02358.1, ECO:0000313|Proteomes:UP000011603}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33500 {ECO:0000313|EMBL:EMA02358.1}, and ATCC 33500 / DSM
RC 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4
RC {ECO:0000313|Proteomes:UP000011603};
RX PubMed=25393412; DOI=10.1371/journal.pgen.1004784;
RA Becker E.A., Seitzer P.M., Tritt A., Larsen D., Krusor M., Yao A.I., Wu D.,
RA Madern D., Eisen J.A., Darling A.E., Facciotti M.T.;
RT "Phylogenetically driven sequencing of extremely halophilic archaea reveals
RT strategies for static and dynamic osmo-response.";
RL PLoS Genet. 10:E1004784-E1004784(2014).
RN [5] {ECO:0000313|EMBL:AHZ22236.1, ECO:0000313|Proteomes:UP000027075}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33500 {ECO:0000313|EMBL:AHZ22236.1}, and ATCC 33500 / DSM
RC 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4
RC {ECO:0000313|Proteomes:UP000027075};
RA Bautista V.;
RT "Transcriptional profiles of Haloferax mediterranei on the basis of
RT nitrogen availability.";
RL Submitted (APR-2014) to the EMBL/GenBank/DDBJ databases.
RN [6] {ECO:0000313|EMBL:AFK18368.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=CGMCC 1.2087;
RA Wang L., Yang H., Xiang H.;
RL Submitted (MAY-2014) to the EMBL/GenBank/DDBJ databases.
RN [7] {ECO:0000313|EMBL:QCQ74879.1, ECO:0000313|Proteomes:UP000299011}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33500 {ECO:0000313|EMBL:QCQ74879.1}, and ATCC 33500 / DSM
RC 1411 / JCM 8866 / NBRC 14739 / NCIMB 2177 / R-4
RC {ECO:0000313|Proteomes:UP000299011};
RA DasSarma S., DasSarma P., DasSarma S., Fomenkov A., Vincze T., Anton B.P.,
RA Roberts R.J.;
RT "Methylomes of two halophilic Archaea, Haloarcula marismortui and Haloferax
RT mediterranei.";
RL Submitted (APR-2019) to the EMBL/GenBank/DDBJ databases.
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; CP001868; AFK18368.1; -; Genomic_DNA.
DR EMBL; CP007551; AHZ22236.1; -; Genomic_DNA.
DR EMBL; AOLO01000007; EMA02358.1; -; Genomic_DNA.
DR EMBL; CP039139; QCQ74879.1; -; Genomic_DNA.
DR RefSeq; WP_004057583.1; NZ_CP039139.1.
DR AlphaFoldDB; I3R2A8; -.
DR STRING; 523841.HFX_0644; -.
DR PaxDb; 523841-HFX_0644; -.
DR GeneID; 40156004; -.
DR KEGG; hme:HFX_0644; -.
DR PATRIC; fig|523841.21.peg.1465; -.
DR eggNOG; arCOG01527; Archaea.
DR eggNOG; arCOG06234; Archaea.
DR HOGENOM; CLU_002929_1_4_2; -.
DR OrthoDB; 30963at2157; -.
DR Proteomes; UP000006469; Chromosome.
DR Proteomes; UP000011603; Unassembled WGS sequence.
DR Proteomes; UP000027075; Chromosome.
DR Proteomes; UP000299011; 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:0006281; P:DNA repair; IEA:InterPro.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR CDD; cd00186; TOP1Ac; 1.
DR CDD; cd03362; TOPRIM_TopoIA_TopoIII; 1.
DR Gene3D; 3.40.50.140; -; 1.
DR Gene3D; 1.10.150.20; 5' to 3' exonuclease, C-terminal subdomain; 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; IPR003583; Hlx-hairpin-Hlx_DNA-bd_motif.
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; IPR028612; Topoisom_1_IA.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034144; TOPRIM_TopoIII.
DR PANTHER; PTHR11390:SF26; DNA TOPOISOMERASE 1; 1.
DR PANTHER; PTHR11390; PROKARYOTIC DNA TOPOISOMERASE; 1.
DR Pfam; PF14520; HHH_5; 1.
DR Pfam; PF01131; Topoisom_bac; 1.
DR Pfam; PF01751; Toprim; 1.
DR Pfam; PF01396; zf-C4_Topoisom; 2.
DR PRINTS; PR00417; PRTPISMRASEI.
DR SMART; SM00278; HhH1; 1.
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 Repeat {ECO:0000256|ARBA:ARBA00022737};
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 5..140
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT REGION 193..198
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT REGION 362..392
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 831..855
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 326
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 52
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 165
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 169
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 328
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
FT SITE 515
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00952"
SQ SEQUENCE 855 AA; 94827 MW; 25C2EBF41385F2A8 CRC64;
MSRGPELIIT EKDNAARRIA DILSGETASA ERMNGVNVYK WGGKRCIGLS GHVVGVDFPP
EYNDWRDVEP VELISAPVEK HPTQENIVAA LRRLARKAGN VTIATDYDRE GELIGKEAYE
LVRDVNEDVP VDRVRFSSIT KREVTEAFEN PDDLDFDLAA AGEARQIIDL VWGAALTRFL
SLSARQLGND FISVGRVQGP TLKLIVDRER EIEAFDPEDY WELFSKLTKD ADGAAESFEA
QYFYLDDDGT EAERIWDEEA AESAYETLLD VDAAEVTAVK RRTRTDKPPA PFNTTQFIRA
AGSIGYSAQR AMSIAEDLYT AGYITYPRTD NTVYPDDLDP RELLGAFEGD RRFKEDAKSL
LEQEEIEPTE GDNETTDHPP IHPTGELPSA SDLTEDEWDV YELVVRRFFA TVAENAVWEH
LRVVAEAAGL SLKANGKRLL EPGYHEVYPY FNSTESFVPD VEEGEALVLS ETHLDAKQTQ
PPRRYGQSRL IETMEQMGIG TKATRHDVIQ KLYDRGYIES DPPRPTRLAR AVVEASEDFA
KLIVSEEMTS QLESDMLAIA RGEATLEDVT EESKEMLGDV FEGLMESREE LGKQLQDSLK
ADKTVGTCPD CGGDLVVRKS RRGSYFIGCD SYPDCTYTLP LPSTGKPLIM EDACEEHDLH
HIKMLAGRKT FVHGCPLCKA EEADEEDDLI IGSCPECGEG ATSEASQGEG GETAEAGGEL
AIKRLRSGSR LVGCTRYPDC DYSLPLPRRG DIEVTDESCE EHDLPELRIT YEGDREPWDL
GCPICNYREY QAQQNGEGGS DLESIKGIGA KTAEKLKDAG IEDVKTLKAA EPDDVASRVD
GVGADTVRKW QTAAD
//
