TOP1P_XYLFA
ID TOP1P_XYLFA Reviewed; 660 AA.
AC Q9PHK2;
DT 20-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 141.
DE RecName: Full=DNA topoisomerase I, plasmid {ECO:0000255|HAMAP-Rule:MF_00952};
DE EC=5.6.2.1 {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 OrderedLocusNames=XF_a0003;
OS Xylella fastidiosa (strain 9a5c).
OG Plasmid pXF51.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Xylella.
OX NCBI_TaxID=160492;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=9a5c;
RX PubMed=10910347; DOI=10.1038/35018003;
RA Simpson A.J.G., Reinach F.C., Arruda P., Abreu F.A., Acencio M.,
RA Alvarenga R., Alves L.M.C., Araya J.E., Baia G.S., Baptista C.S.,
RA Barros M.H., Bonaccorsi E.D., Bordin S., Bove J.M., Briones M.R.S.,
RA Bueno M.R.P., Camargo A.A., Camargo L.E.A., Carraro D.M., Carrer H.,
RA Colauto N.B., Colombo C., Costa F.F., Costa M.C.R., Costa-Neto C.M.,
RA Coutinho L.L., Cristofani M., Dias-Neto E., Docena C., El-Dorry H.,
RA Facincani A.P., Ferreira A.J.S., Ferreira V.C.A., Ferro J.A., Fraga J.S.,
RA Franca S.C., Franco M.C., Frohme M., Furlan L.R., Garnier M., Goldman G.H.,
RA Goldman M.H.S., Gomes S.L., Gruber A., Ho P.L., Hoheisel J.D.,
RA Junqueira M.L., Kemper E.L., Kitajima J.P., Krieger J.E., Kuramae E.E.,
RA Laigret F., Lambais M.R., Leite L.C.C., Lemos E.G.M., Lemos M.V.F.,
RA Lopes S.A., Lopes C.R., Machado J.A., Machado M.A., Madeira A.M.B.N.,
RA Madeira H.M.F., Marino C.L., Marques M.V., Martins E.A.L., Martins E.M.F.,
RA Matsukuma A.Y., Menck C.F.M., Miracca E.C., Miyaki C.Y.,
RA Monteiro-Vitorello C.B., Moon D.H., Nagai M.A., Nascimento A.L.T.O.,
RA Netto L.E.S., Nhani A. Jr., Nobrega F.G., Nunes L.R., Oliveira M.A.,
RA de Oliveira M.C., de Oliveira R.C., Palmieri D.A., Paris A., Peixoto B.R.,
RA Pereira G.A.G., Pereira H.A. Jr., Pesquero J.B., Quaggio R.B.,
RA Roberto P.G., Rodrigues V., de Rosa A.J.M., de Rosa V.E. Jr., de Sa R.G.,
RA Santelli R.V., Sawasaki H.E., da Silva A.C.R., da Silva A.M.,
RA da Silva F.R., Silva W.A. Jr., da Silveira J.F., Silvestri M.L.Z.,
RA Siqueira W.J., de Souza A.A., de Souza A.P., Terenzi M.F., Truffi D.,
RA Tsai S.M., Tsuhako M.H., Vallada H., Van Sluys M.A., Verjovski-Almeida S.,
RA Vettore A.L., Zago M.A., Zatz M., Meidanis J., Setubal J.C.;
RT "The genome sequence of the plant pathogen Xylella fastidiosa.";
RL Nature 406:151-159(2000).
RN [2]
RP DISCUSSION OF SEQUENCE.
RX PubMed=11407914; DOI=10.1006/plas.2000.1514;
RA Marques M.V., da Silva A.M., Gomes S.L.;
RT "Genetic organization of Plasmid pXF51 from the plant pathogen Xylella
RT fastidiosa.";
RL Plasmid 45:184-199(2001).
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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AE003851; AAF85572.1; -; Genomic_DNA.
DR PIR; C82861; C82861.
DR RefSeq; WP_010895200.1; NC_002490.1.
DR AlphaFoldDB; Q9PHK2; -.
DR SMR; Q9PHK2; -.
DR STRING; 160492.XF_a0003; -.
DR EnsemblBacteria; AAF85572; AAF85572; XF_a0003.
DR KEGG; xfa:XF_a0003; -.
DR eggNOG; COG0550; Bacteria.
DR HOGENOM; CLU_002929_4_3_6; -.
DR OMA; RLVGYMV; -.
DR Proteomes; UP000000812; Plasmid pXF51.
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; 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; IPR013498; Topo_IA_Znf.
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 Pfam; PF01396; zf-C4_Topoisom; 2.
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 3: Inferred from homology;
KW DNA-binding; Isomerase; Magnesium; Metal-binding; Plasmid;
KW Reference proteome; Repeat; Topoisomerase; Zinc; Zinc-finger.
FT CHAIN 1..660
FT /note="DNA topoisomerase I, plasmid"
FT /id="PRO_0000145174"
FT DOMAIN 1..110
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT ZN_FING 563..589
FT /note="C4-type 1"
FT ZN_FING 613..643
FT /note="C4-type 2"
FT REGION 158..163
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT ACT_SITE 287
FT /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT BINDING 7
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 79
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 79
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT BINDING 81
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 31
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 134
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 135
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 138
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 143
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 289
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT SITE 483
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
SQ SEQUENCE 660 AA; 72556 MW; AC4A5F000A503A1F CRC64;
MKLMIIESPG KIEKLSTILG DGWKIAASVG HVRDLPQKEM GVAAPDFKPS YELTERGEGV
VAKLKNLLKQ ADSVYLATDP DREGEAISWH LQQCLKLSNP LRVTFNEITA NAVKASLVAP
RTIDVKRVAA QEARRVLDRL VGYMVSPELS RLTGKRLSAG RVQSPAVRLV VEREREIKAF
KVTNHFGAML FFADAKTSGE WSAEWLTKPK FVAEDNPYFM DRDFAAAVAQ VKAVVVKSFD
ESEAKRSPPP PFTTSTMQQA ASVTLGVDPK AAMDAAQKLY EQGHITYHRT DNPNVSDESL
GDIYAVSVKL GLDIAEKPRK FKAPAGAQVG HPAVTPTHWE VEEAGETSDQ KALYKLIRLR
AIACQLADAR YAVRTVRLEA AQPVGGKNVE FEARGRTLIY QGWLKLIAGD QTEEEDGNEK
ESSNPIPVCA PGECLDVARG KLLEKKTKPP SHYTQATLVK KLESEGIGRP ATYAAIMDNI
VSRGYVKTEK KYLFPTETGE LIVDSLVGKF EFLDLGFTRE IEESLDRIAQ GESGYKAVIA
KVHDQLNMEL STLQVSATPK HPCQECGKPL RRIPGKNGHF WGCSGYPDCS VTFPDEGGKP
GQKKPVEVSN FACVKCGNPL KHLVKKGKGG YDFWGCSGFK EGCKATYEDK KGKPNFEKAK
