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Protein

DNA topoisomerase 1

Gene

topA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 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 annotationNote: Binds two Mg2+ per subunit.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi9 – 91Magnesium 1; catalyticUniRule annotation
Sitei33 – 331Interaction with DNAUniRule annotation
Metal bindingi82 – 821Magnesium 1; catalyticUniRule annotation
Metal bindingi82 – 821Magnesium 2UniRule annotation
Metal bindingi84 – 841Magnesium 2UniRule annotation
Sitei139 – 1391Interaction with DNAUniRule annotation
Sitei140 – 1401Interaction with DNAUniRule annotation
Sitei143 – 1431Interaction with DNAUniRule annotation
Sitei148 – 1481Interaction with DNAUniRule annotation
Sitei155 – 1551Interaction with DNAUniRule annotation
Active sitei298 – 2981O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
Sitei300 – 3001Interaction with DNAUniRule annotation
Sitei490 – 4901Interaction with DNAUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri579 – 60527C4-type 1Add
BLAST
Zinc fingeri619 – 64729C4-type 2Add
BLAST
Zinc fingeri660 – 68324C4-type 3Add
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciBSUB:BSU16120-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 1UniRule annotation (EC:5.99.1.2UniRule annotation)
Alternative name(s):
DNA topoisomerase IUniRule annotation
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
Gene namesi
Name:topAUniRule annotation
Synonyms:topI
Ordered Locus Names:BSU16120
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001570 Componenti: Chromosome

Organism-specific databases

GenoListiBSU16120. [Micado]

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 691691DNA topoisomerase 1PRO_0000145142Add
BLAST

Proteomic databases

PaxDbiP39814.

Interactioni

Subunit structurei

Monomer.UniRule annotation

Protein-protein interaction databases

STRINGi224308.BSU16120.

Structurei

3D structure databases

ProteinModelPortaliP39814.
SMRiP39814. Positions 2-617.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini3 – 114112ToprimUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni163 – 1686Interaction with DNAUniRule annotation

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri579 – 60527C4-type 1Add
BLAST
Zinc fingeri619 – 64729C4-type 2Add
BLAST
Zinc fingeri660 – 68324C4-type 3Add
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG0551.
HOGENOMiHOG000004018.
InParanoidiP39814.
KOiK03168.
OMAiVVECDKC.
OrthoDBiEOG6S7XQ9.
PhylomeDBiP39814.

Family and domain databases

Gene3Di1.10.460.10. 3 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_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.
IPR013498. Topo_IA_Znf.
IPR005733. TopoI_bac-type.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 2 hits.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 2 hits.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P39814-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDYLVIVES PAKAKTIERY LGKKYKVKAS MGHVRDLPKS QMGVDIEQNF
60 70 80 90 100
EPKYITIRGK GPVLKELKTA AKKAKKVYLA ADPDREGEAI AWHLAHSLDL
110 120 130 140 150
DLNSDCRVVF NEITKDAIKE SFKHPRMINM DLVDAQQARR ILDRLVGYKI
160 170 180 190 200
SPILWKKVKK GLSAGRVQSV ALRLIIDREK EINDFKPEEY WTIDGTFLKG
210 220 230 240 250
QETFEASFFG KNGKKLPLNS EADVKEILSQ LKGNQYTVEK VTKKERKRNP
260 270 280 290 300
ALPFTTSTLQ QEAARKLNFR AKKTMMIAQQ LYEGIDLGRE GTVGLITYMR
310 320 330 340 350
TDSTRISNTA VDEAAAFIDQ TYGKEFLGGK RKPAKKNENA QDAHEAIRPT
360 370 380 390 400
SVLRKPSELK AVLGRDQMRL YKLIWERFVA SQMAPAVLDT MSVDLTNNGL
410 420 430 440 450
TFRANGSKVK FSGFMKVYVE GKDDQMEEKD RMLPDLQEGD TVLSKDIEPE
460 470 480 490 500
QHFTQPPPRY TEARLVKTLE ERGIGRPSTY APTLDTIQRR GYVALDNKRF
510 520 530 540 550
VPTELGQIVL DLIMEFFPEI INVEFTAKME RDLDHVEEGN TEWVKIIDNF
560 570 580 590 600
YTDFEKRVKK AESEMKEVEI EPEYAGEDCE LCSSPMVYKM GRYGKFLACS
610 620 630 640 650
NFPDCRNTKP IVKQIGVKCP SCGEGNIVER KSKKKRVFYG CDRYPDCEFV
660 670 680 690
SWDKPIERKC PKCGKMLVEK KLKKGIQVQC VECDYKEEPQ K
Length:691
Mass (Da):79,078
Last modified:February 1, 1995 - v1
Checksum:i58A45C84E52711BB
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L27797 Genomic DNA. Translation: AAA22763.1.
AJ000975 Genomic DNA. Translation: CAA04422.1.
AL009126 Genomic DNA. Translation: CAB13485.1.
PIRiG69724.
RefSeqiNP_389494.1. NC_000964.3.
WP_003245599.1. NZ_JNCM01000035.1.

Genome annotation databases

EnsemblBacteriaiCAB13485; CAB13485; BSU16120.
GeneIDi937982.
KEGGibsu:BSU16120.
PATRICi18975029. VBIBacSub10457_1706.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L27797 Genomic DNA. Translation: AAA22763.1.
AJ000975 Genomic DNA. Translation: CAA04422.1.
AL009126 Genomic DNA. Translation: CAB13485.1.
PIRiG69724.
RefSeqiNP_389494.1. NC_000964.3.
WP_003245599.1. NZ_JNCM01000035.1.

3D structure databases

ProteinModelPortaliP39814.
SMRiP39814. Positions 2-617.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.BSU16120.

Proteomic databases

PaxDbiP39814.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB13485; CAB13485; BSU16120.
GeneIDi937982.
KEGGibsu:BSU16120.
PATRICi18975029. VBIBacSub10457_1706.

Organism-specific databases

GenoListiBSU16120. [Micado]

Phylogenomic databases

eggNOGiCOG0551.
HOGENOMiHOG000004018.
InParanoidiP39814.
KOiK03168.
OMAiVVECDKC.
OrthoDBiEOG6S7XQ9.
PhylomeDBiP39814.

Enzyme and pathway databases

BioCyciBSUB:BSU16120-MONOMER.

Family and domain databases

Gene3Di1.10.460.10. 3 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_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.
IPR013498. Topo_IA_Znf.
IPR005733. TopoI_bac-type.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 2 hits.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 2 hits.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and sequencing of the TopI gene, the gene encoding B. subtilis DNA topoisomerase I."
    de Jong S.
    Submitted (AUG-1994) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168 / 8G5.
  2. "Cloning and sequencing 7.5 Kbp of DNA from Bacillus subtilis upstream of the codV gene."
    Foulger D., Errington J.
    Submitted (OCT-1997) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 168.
  3. "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 nameiTOP1_BACSU
AccessioniPrimary (citable) accession number: P39814
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: May 27, 2015
This is version 122 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.