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Protein

DNA topoisomerase 3

Gene

topB

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.UniRule annotation

Catalytic activityi

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.UniRule annotation

Cofactori

Mg2+UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi9 – 91Magnesium; catalyticUniRule annotation
Sitei61 – 611Interaction with DNAUniRule annotation
Metal bindingi105 – 1051Magnesium; catalyticUniRule annotation
Sitei168 – 1681Interaction with DNAUniRule annotation
Sitei176 – 1761Interaction with DNAUniRule annotation
Active sitei310 – 3101O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
Sitei312 – 3121Interaction with DNAUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciBSUB:BSU04260-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 3UniRule annotation (EC:5.99.1.2UniRule annotation)
Alternative name(s):
DNA topoisomerase IIIUniRule annotation
Gene namesi
Name:topBUniRule annotation
Ordered Locus Names:BSU04260
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU04260. [Micado]

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 727727DNA topoisomerase 3PRO_0000286366Add
BLAST

Proteomic databases

PaxDbiP96583.

Interactioni

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100002418.

Structurei

3D structure databases

ProteinModelPortaliP96583.
SMRiP96583. Positions 5-626.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 136134ToprimUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni187 – 1926Interaction with DNAUniRule annotation

Sequence similaritiesi

Belongs to the type IA topoisomerase family.UniRule annotation
Contains 1 Toprim domain.UniRule annotation

Phylogenomic databases

eggNOGiCOG0551.
HOGENOMiHOG000086847.
InParanoidiP96583.
KOiK03169.
OMAiTKHDEYF.
OrthoDBiEOG60CWM6.
PhylomeDBiP96583.

Family and domain databases

Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00953. Topoisom_3_prok.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013825. Topo_IA_cen_sub2.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd_dom.
IPR005738. TopoIII.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01056. topB. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P96583-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKTVVLAEK PSVGRDLARV LKCHKKGNGY LEGDQYIVTW ALGHLVTLAD
60 70 80 90 100
PEGYGKEFQS WRLEDLPIIP EPLKLVVIKK TGKQFNAVKS QLTRKDVNQI
110 120 130 140 150
VIATDAGREG ELVARWIIEK ANVRKPIKRL WISSVTDKAI KEGFQKLRSG
160 170 180 190 200
KEYENLYHSA VARAEADWIV GINATRALTT KFNAQLSCGR VQTPTLAMIA
210 220 230 240 250
KREADIQAFT PVPYYGIRAA VDGMTLTWQD KKSKQTRTFN QDVTSRLLKN
260 270 280 290 300
LQGKQAVVAE LKKTAKKSFA PALYDLTELQ RDAHKRFGFS AKETLSVLQK
310 320 330 340 350
LYEQHKLVTY PRTDSRFLSS DIVPTLKDRL EGMEVKPYAQ YVSQIKKRGI
360 370 380 390 400
KSHKGYVNDA KVSDHHAIIP TEEPLVLSSL SDKERKLYDL IAKRFLAVLM
410 420 430 440 450
PAFEYEETKV IAEIGGETFT AKGKTVQSQG WKAVYDMAEE DDEQEDDRDQ
460 470 480 490 500
TLPALQKGDT LAVRTLTETS GQTKPPARFN EGTLLSAMEN PSAFMQGEEK
510 520 530 540 550
GLVKTLGETG GLGTVATRAD IIEKLFNSFL IEKKGQDIFI TSKGKQLLQL
560 570 580 590 600
VPEDLKSPAL TAEWEQKLSA IAAGKLKSAV FIKDMKAYAH QTVKEIKNSS
610 620 630 640 650
QTFRHDNITG TACPECGKMM LKVNGKRGTM LVCQDRECGS RKTIARKTNA
660 670 680 690 700
RCPNCHKRME LRGQGEGQTF ACVCGHREKL SVFEKRKNKD KARATKRDVS
710 720
SYMKKQNKDE PINNALAEQL KKLGLDK
Length:727
Mass (Da):81,477
Last modified:May 1, 1997 - v1
Checksum:i7146120F257C5FF3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB001488 Genomic DNA. Translation: BAA19263.1.
AL009126 Genomic DNA. Translation: CAB12233.1.
PIRiH69724.
RefSeqiNP_388307.1. NC_000964.3.
WP_003246684.1. NZ_JNCM01000031.1.

Genome annotation databases

EnsemblBacteriaiCAB12233; CAB12233; BSU04260.
GeneIDi938247.
KEGGibsu:BSU04260.
PATRICi18972430. VBIBacSub10457_0443.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB001488 Genomic DNA. Translation: BAA19263.1.
AL009126 Genomic DNA. Translation: CAB12233.1.
PIRiH69724.
RefSeqiNP_388307.1. NC_000964.3.
WP_003246684.1. NZ_JNCM01000031.1.

3D structure databases

ProteinModelPortaliP96583.
SMRiP96583. Positions 5-626.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100002418.

Chemistry

BindingDBiP96583.
ChEMBLiCHEMBL4320.

Proteomic databases

PaxDbiP96583.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12233; CAB12233; BSU04260.
GeneIDi938247.
KEGGibsu:BSU04260.
PATRICi18972430. VBIBacSub10457_0443.

Organism-specific databases

GenoListiBSU04260. [Micado]

Phylogenomic databases

eggNOGiCOG0551.
HOGENOMiHOG000086847.
InParanoidiP96583.
KOiK03169.
OMAiTKHDEYF.
OrthoDBiEOG60CWM6.
PhylomeDBiP96583.

Enzyme and pathway databases

BioCyciBSUB:BSU04260-MONOMER.

Miscellaneous databases

PROiP96583.

Family and domain databases

Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00953. Topoisom_3_prok.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013825. Topo_IA_cen_sub2.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd_dom.
IPR005738. TopoIII.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01056. topB. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "A 148 kbp sequence of the region between 35 and 47 degree of the Bacillus subtilis genome."
    Kasahara Y., Nakai S., Lee S., Sadaie Y., Ogasawara N.
    Submitted (MAR-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
    Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
    , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
    Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 168.

Entry informationi

Entry nameiTOP3_BACSU
AccessioniPrimary (citable) accession number: P96583
Secondary accession number(s): Q797M6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 2007
Last sequence update: May 1, 1997
Last modified: June 24, 2015
This is version 101 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.