ID V7AD46_PHAVU Unreviewed; 924 AA.
AC V7AD46;
DT 19-FEB-2014, integrated into UniProtKB/TrEMBL.
DT 19-FEB-2014, sequence version 1.
DT 27-MAR-2024, entry version 47.
DE RecName: Full=DNA topoisomerase I {ECO:0000256|RuleBase:RU365101};
DE EC=5.6.2.1 {ECO:0000256|RuleBase:RU365101};
DE AltName: Full=DNA topoisomerase 1 {ECO:0000256|RuleBase:RU365101};
GN ORFNames=PHAVU_011G016600g {ECO:0000313|EMBL:ESW03467.1};
OS Phaseolus vulgaris (Kidney bean) (French bean).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Phaseolus.
OX NCBI_TaxID=3885 {ECO:0000313|EMBL:ESW03467.1, ECO:0000313|Proteomes:UP000000226};
RN [1] {ECO:0000313|EMBL:ESW03467.1}
RP NUCLEOTIDE SEQUENCE.
RA Schmutz J., McClean P., Shu S., Cregan P., Rokhsar D., Jackson S.;
RL Submitted (APR-2013) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|Proteomes:UP000000226}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. G19833 {ECO:0000313|Proteomes:UP000000226};
RX PubMed=24908249; DOI=10.1038/ng.3008;
RA Schmutz J., McClean P.E., Mamidi S., Wu G.A., Cannon S.B., Grimwood J.,
RA Jenkins J., Shu S., Song Q., Chavarro C., Torres-Torres M., Geffroy V.,
RA Moghaddam S.M., Gao D., Abernathy B., Barry K., Blair M., Brick M.A.,
RA Chovatia M., Gepts P., Goodstein D.M., Gonzales M., Hellsten U.,
RA Hyten D.L., Jia G., Kelly J.D., Kudrna D., Lee R., Richard M.M.,
RA Miklas P.N., Osorno J.M., Rodrigues J., Thareau V., Urrea C.A., Wang M.,
RA Yu Y., Zhang M., Wing R.A., Cregan P.B., Rokhsar D.S., Jackson S.A.;
RT "A reference genome for common bean and genome-wide analysis of dual
RT domestications.";
RL Nat. Genet. 46:707-713(2014).
CC -!- FUNCTION: Releases the supercoiling and torsional tension of DNA
CC introduced during the DNA replication and transcription by transiently
CC cleaving and rejoining one strand of the DNA duplex. Introduces a
CC single-strand break via transesterification at the specific target site
CC 5'-[CT]CCTTp site in duplex DNA. The scissile phosphodiester is
CC attacked by the catalytic tyrosine of the enzyme, resulting in the
CC formation of a DNA-(3'-phosphotyrosyl)-enzyme intermediate and the
CC expulsion of a 5'-OH DNA strand. The free DNA strand then undergoes
CC passage around the unbroken strand thus removing DNA supercoils.
CC Finally, in the religation step, the DNA 5'-OH attacks the covalent
CC intermediate to expel the active-site tyrosine and restore the DNA
CC phosphodiester backbone. {ECO:0000256|RuleBase:RU365101}.
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,
CC ECO:0000256|RuleBase:RU365101};
CC -!- SIMILARITY: Belongs to the type IB topoisomerase family.
CC {ECO:0000256|ARBA:ARBA00006645, ECO:0000256|RuleBase:RU365101}.
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DR EMBL; CM002298; ESW03467.1; -; Genomic_DNA.
DR EMBL; CM002298; ESW03468.1; -; Genomic_DNA.
DR RefSeq; XP_007131473.1; XM_007131411.1.
DR RefSeq; XP_007131474.1; XM_007131412.1.
DR AlphaFoldDB; V7AD46; -.
DR STRING; 3885.V7AD46; -.
DR EnsemblPlants; ESW03467; ESW03467; PHAVU_011G016600g.
DR EnsemblPlants; ESW03468; ESW03468; PHAVU_011G016600g.
DR GeneID; 18614861; -.
DR Gramene; ESW03467; ESW03467; PHAVU_011G016600g.
DR Gramene; ESW03468; ESW03468; PHAVU_011G016600g.
DR KEGG; pvu:PHAVU_011G016600g; -.
DR eggNOG; KOG0981; Eukaryota.
DR OMA; GECPVTT; -.
DR OrthoDB; 10940at2759; -.
DR Proteomes; UP000000226; Chromosome 11.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003917; F:DNA topoisomerase type I (single strand cut, ATP-independent) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR CDD; cd00659; Topo_IB_C; 1.
DR CDD; cd00660; Topoisomer_IB_N; 1.
DR Gene3D; 1.10.132.10; -; 1.
DR Gene3D; 2.170.11.10; DNA Topoisomerase I, domain 2; 1.
DR Gene3D; 1.10.10.41; Yeast DNA topoisomerase - domain 1; 1.
DR InterPro; IPR011010; DNA_brk_join_enz.
DR InterPro; IPR013034; DNA_topo_DNA_db_N_dom1.
DR InterPro; IPR013030; DNA_topo_DNA_db_N_dom2.
DR InterPro; IPR001631; TopoI.
DR InterPro; IPR018521; TopoI_AS.
DR InterPro; IPR025834; TopoI_C_dom.
DR InterPro; IPR014711; TopoI_cat_a-hlx-sub_euk.
DR InterPro; IPR014727; TopoI_cat_a/b-sub_euk.
DR InterPro; IPR013500; TopoI_cat_euk.
DR InterPro; IPR008336; TopoI_DNA-bd_euk.
DR InterPro; IPR036202; TopoI_DNA-bd_euk_N_sf.
DR InterPro; IPR013499; TopoI_euk.
DR PANTHER; PTHR10290:SF23; DNA TOPOISOMERASE 1; 1.
DR PANTHER; PTHR10290; DNA TOPOISOMERASE I; 1.
DR Pfam; PF14370; Topo_C_assoc; 1.
DR Pfam; PF01028; Topoisom_I; 1.
DR Pfam; PF02919; Topoisom_I_N; 1.
DR PRINTS; PR00416; EUTPISMRASEI.
DR SMART; SM00435; TOPEUc; 1.
DR SUPFAM; SSF56349; DNA breaking-rejoining enzymes; 1.
DR SUPFAM; SSF56741; Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment; 1.
DR PROSITE; PS00176; TOPOISOMERASE_I_EUK; 1.
PE 3: Inferred from homology;
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125, ECO:0000256|RuleBase:RU365101};
KW Isomerase {ECO:0000256|ARBA:ARBA00023235, ECO:0000256|RuleBase:RU365101};
KW Reference proteome {ECO:0000313|Proteomes:UP000000226};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029,
KW ECO:0000256|RuleBase:RU365101}.
FT DOMAIN 521..897
FT /note="DNA topoisomerase I eukaryotic-type"
FT /evidence="ECO:0000259|SMART:SM00435"
FT REGION 1..378
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 820..843
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 9..26
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 42..57
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 79..110
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 121..145
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 150..169
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 196..215
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 316..330
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 358..378
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 924 AA; 104534 MW; 8A10B9E8968246C2 CRC64;
MAVETSDKPN LPHDFDDDDD APIIYKRLSA KKNQSLPEAP NLPHDFDDDD DAPIIYKRLS
AKKNQSLSEA RKSSSHIHEG QSYRQIPNAS SSNGQTSSMQ KGNTAPSLKP SAMKPSVGIS
RAPNSVGNTS SVKFPVANSK SPSLADKQKM FIDVKVEPKS TVHSGKDFCE DSEDDEDNKP
LSFRLKNSNH DNKVTSVVKK SYEDSDGDDD VPLSKKLPRN FNLGTSSSNH DDSDKKPISK
IQKERQNGSG MSNKQDRPSL LPAKRPLDNS NSLHPSVKKP KVSGSDASIK TKPGFQKREL
KLEDDDDDDD IPISQRIKKQ TVSGDKSSSM KKVITKVAKV NKSSSKSFKK QTKKPVKKSG
SGSEYSKSSK LLPSSGDGQK KWTTLVHNGV IFPPPYQRHG VKMLYKGRPV DLTPEQEEVA
TMYAVMRDTE YMQKDKFKDN FWSDWRKLLG RNHVIQNLKD CDFTPIYDWY QSEKEKKKQM
TTDEKKTVKE EKMKQEEKYM WAIVDGVKEK VGNFRVEPPG LFRGRGEHPK MGKLKKRIHP
GDITINIGKD APIPECPIPG ERWKEIRHDN TVTWLAYWSD PINPKLFKYV FLAASSSLKG
QSDKEKYEKA RMLKDYIENI RSAYTKDFTN KDITKLQIAV ATYLIDKLAL RAGNEKDDDE
ADTVGCCTLK VENVIREPPN KLKFNFLGKD SIKYENTVEV ELPVYNAILK LQKDKRPGDD
LFDKLDTSKL NAHLKELMPG LTAKVFRTFN ASITLDNMLN KGTKDGDVGE KIVVYQHANK
QVAIICNHQR SVSKSHDAQM SKLTEKIDEL QAVLKELKTD LDRARKGKPP SKSSDGKTKK
NLTPEVLEKK ISQTNAKIEK MQRDMKTKED LKTVALGTSK INYLDPRITV AWCKRHEVPI
EKIFNKSLLA KFCWAMDVDP DFRF
//
