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Protein

DNA topoisomerase 3

Gene

topB

Organism
Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46)
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

BioCyciBLIC279010:GJ2P-506-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:BLi00518, BL02823
OrganismiBacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46)
Taxonomic identifieri279010 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000000606 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 727727DNA topoisomerase 3PRO_0000286364Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi279010.BLi00518.

Structurei

3D structure databases

ProteinModelPortaliQ65N90.
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.
KOiK03169.
OrthoDBiEOG60CWM6.

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.

Q65N90-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKTVVLAEK PSVGRDLARV LKCHKKGNGY LEGDRYIVTW ALGHLVTLAD
60 70 80 90 100
PEGYGKEYQS WRLEDLPIIP EPLKLVVIKK TGKQFQAVKS QLIRKDVKDI
110 120 130 140 150
VIATDAGREG ELVARWIIEK AKVTKPLKRL WISSVTDKAI KDGFKNLKNG
160 170 180 190 200
KDFENLYHSA VARAEADWIV GINATRALTT KFNAQLSCGR VQTPTLAMIA
210 220 230 240 250
KREEDIKNFK PVPYFGLRAA VDGMTLTWQD KKTSQTRTFN ASVTSQLAGA
260 270 280 290 300
LQGKPAVIVD LKKTAKKSFA PGLYDLTELQ RDAHKRFGFS AKETLSVLQK
310 320 330 340 350
LYEQHKLVTY PRTDSRFLSN DIVPTLKDRL EGMQVKPYAQ HVARILKRGV
360 370 380 390 400
KANKSFVNDA KVSDHHAIIP TEEPLALGAL SEKERKLYDL IAKRFLAVLM
410 420 430 440 450
PPFEYEETKV FAEIGGETFT AKGKTVQSQG WKAVYDFADE DDDEEEKDQT
460 470 480 490 500
LPKLAKGDTL SVRSLTETKG ETKPPARFNE GTLLSAMENP AAFMQGEEKN
510 520 530 540 550
LVKTLGETGG LGTVATRADI IEKLFNTFLI EKKGKDIYIT SKGKQLLELV
560 570 580 590 600
PSDLKSPALT AEWEQKLSGI AKGKLKSSAF IKEMKEYAKQ TIREIKSSNQ
610 620 630 640 650
KFKHDNITGT HCPDCGKLML KVNGKRGTML VCQDRECGHR KTVAKQTNAR
660 670 680 690 700
CPVCHKRMEL RGHGEGQTFA CVCGHREKLS VFEKRRAKDK NSKASKRDVH
710 720
SYMKKQNKDE PINNALAEQL KKLKLDQ
Length:727
Mass (Da):81,504
Last modified:May 1, 2007 - v2
Checksum:i6649802B7503A542
GO

Sequence cautioni

The sequence AAU22114.2 differs from that shown. Reason: Erroneous initiation. Curated
The sequence AAU39474.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017333 Genomic DNA. Translation: AAU39474.1. Different initiation.
CP000002 Genomic DNA. Translation: AAU22114.2. Different initiation.
RefSeqiYP_006711945.1. NC_006322.1.
YP_077752.2. NC_006270.3.

Genome annotation databases

EnsemblBacteriaiAAU22114; AAU22114; BL02823.
AAU39474; AAU39474; BLi00518.
KEGGibld:BLi00518.
bli:BL02823.
PATRICi18946539. VBIBacLic203714_0508.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE017333 Genomic DNA. Translation: AAU39474.1. Different initiation.
CP000002 Genomic DNA. Translation: AAU22114.2. Different initiation.
RefSeqiYP_006711945.1. NC_006322.1.
YP_077752.2. NC_006270.3.

3D structure databases

ProteinModelPortaliQ65N90.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi279010.BLi00518.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAU22114; AAU22114; BL02823.
AAU39474; AAU39474; BLi00518.
KEGGibld:BLi00518.
bli:BL02823.
PATRICi18946539. VBIBacLic203714_0508.

Phylogenomic databases

eggNOGiCOG0551.
HOGENOMiHOG000086847.
KOiK03169.
OrthoDBiEOG60CWM6.

Enzyme and pathway databases

BioCyciBLIC279010:GJ2P-506-MONOMER.

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

  1. "The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential."
    Veith B., Herzberg C., Steckel S., Feesche J., Maurer K.H., Ehrenreich P., Baeumer S., Henne A., Liesegang H., Merkl R., Ehrenreich A., Gottschalk G.
    J. Mol. Microbiol. Biotechnol. 7:204-211(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46.

Entry informationi

Entry nameiTOP3_BACLD
AccessioniPrimary (citable) accession number: Q65N90
Secondary accession number(s): Q62YP4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 1, 2007
Last sequence update: May 1, 2007
Last modified: June 24, 2015
This is version 82 of the entry and version 2 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. 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.