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Protein

DNA topoisomerase 1

Gene

topA

Organism
Bacillus pseudofirmus (strain OF4)
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 (By similarity).By similarity

Catalytic activityi

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei48 – 481Interaction with DNAPROSITE-ProRule annotation
Sitei167 – 1671Interaction with DNAPROSITE-ProRule annotation
Sitei171 – 1711Interaction with DNAPROSITE-ProRule annotation
Active sitei323 – 3231O-(5'-phospho-DNA)-tyrosine intermediateBy similarity
Sitei325 – 3251Interaction with DNAPROSITE-ProRule annotation
Sitei529 – 5291Interaction with DNAPROSITE-ProRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciBPSE398511:GJI9-4279-MONOMER.
BPSE398511:GJI9-4280-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA topoisomerase 1 (EC:5.99.1.2)
Alternative name(s):
DNA topoisomerase I
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
Gene namesi
Name:topA
Ordered Locus Names:BpOF4_21279/BpOF4_21284
Encoded oniPlasmid pBpOF4-011 Publication
OrganismiBacillus pseudofirmus (strain OF4)
Taxonomic identifieri398511 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
ProteomesiUP000001544 Componenti: Plasmid pBpOF4-01

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 706706DNA topoisomerase 1PRO_0000145140Add
BLAST

Interactioni

Subunit structurei

Monomer.By similarity

Structurei

3D structure databases

ProteinModelPortaliP34184.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 140140ToprimPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni199 – 2046Interaction with DNABy similarity

Sequence similaritiesi

Belongs to the type IA topoisomerase family.Curated
Contains 1 Toprim domain.PROSITE-ProRule annotation

Family and domain databases

Gene3Di1.10.290.10. 1 hit.
1.10.460.10. 2 hits.
3.40.50.140. 1 hit.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013826. Topo_IA_cen_sub3.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd_dom.
IPR013498. Topo_IA_Znf.
IPR025589. Toprim_C_rpt.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF13342. Toprim_Crpt. 1 hit.
PF01396. zf-C4_Topoisom. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P34184-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYAILAEKPS AAKAYAQALN GKRQGRIYVA PPSSLLPEGA LICAAVGHIL
60 70 80 90 100
EFLEPGELNE KYKSYSLDSL PIIIDLFQYK VVSDKKEVLQ RIKDTIFDKR
110 120 130 140 150
VKTIILATDA AAEGEYIGRN ILYRLQCKKT IKRLWTSSMT ATSIQKAFSQ
160 170 180 190 200
LKADAETLPL YYQAKARAES DYMIGLTLSR AYGILLKEQG IVPHNTTISL
210 220 230 240 250
GRVQTPLLAE IVKRERLIEQ FTAENFWTVK ATFNNQGNVY EGEWFHEKEN
260 270 280 290 300
RIFKEEQAEQ LCELVRNQSS TIMEMKEEMR TYQPPLLYXL STLQMDAGNA
310 320 330 340 350
FGFKPAETLK YAQSLYDKGY LSYPRTQDER ITESDARELE NNIQFLSGHD
360 370 380 390 400
TFGALFPLPV STLMNNKRYI GEVTDHHALL ITDKIPKDKD LSEDEKSIYH
410 420 430 440 450
LVVKRILAAH YPDVAMSHKE IITKVMDRFT FRSKGKELLS KGWHHIIPPT
460 470 480 490 500
NENDIMLPTL LKGSEGVVTD TLTTKSKTKP PNRYTSSSLI GFMKNAAQAI
510 520 530 540 550
EDEDRKSISN LPLGTEATRA GLITLLESRK YIEWKKNKVY PTLLGITVVD
560 570 580 590 600
SIKRGSVIKS PILTAKWDVK LNEIGASLYN HKDFIAHSKK LSSVLFEEVK
610 620 630 640 650
TYSSTWNQNG VERIKSESIG ACLLCGSNVV LRKGKHGEFY GCSNYKDSGC
660 670 680 690 700
TFNLPFKVLN KKLSKKQLME LLKNEKTDII KGFKWKDKTF NAPLVWNRED

QKVQFGK
Length:707
Mass (Da):80,296
Last modified:January 11, 2011 - v3
Checksum:i1E07919E5AD9AA00
GO

Sequence cautioni

The sequence ADC52251.1 differs from that shown.Probable readthrough of the stop codon.Curated
The sequence ADC52252.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence CAA78484.1 differs from that shown.Probable readthrough of the stop codon.Curated
The sequence CAA78485.1 differs from that shown. Reason: Frameshift at position 525. Curated
The sequence CAA78485.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti126 – 1261Q → H in CAA78484 (PubMed:1329032).Curated
Sequence conflicti142 – 1421T → F in CAA78484 (PubMed:1329032).Curated
Sequence conflicti218 – 2181I → L in CAA78484 (PubMed:1329032).Curated
Sequence conflicti254 – 2541K → T in CAA78484 (PubMed:1329032).Curated
Sequence conflicti258 – 2581A → D in CAA78484 (PubMed:1329032).Curated
Sequence conflicti352 – 3521F → S in CAA78485 (PubMed:1329032).Curated
Sequence conflicti443 – 4431W → R in CAA78485 (PubMed:1329032).Curated
Sequence conflicti523 – 5242IT → TH in CAA78485 (PubMed:1329032).Curated
Sequence conflicti548 – 5481V → A in CAA78485 (PubMed:1329032).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001879 Genomic DNA. Translation: ADC52251.1. Sequence problems.
CP001879 Genomic DNA. Translation: ADC52252.1. Different initiation.
Z14112 Genomic DNA. Translation: CAA78484.1. Sequence problems.
Z14112 Genomic DNA. Translation: CAA78485.1. Sequence problems.
PIRiS23866.
RefSeqiYP_003429143.1. NC_013792.1.
YP_003429144.1. NC_013792.1.

Genome annotation databases

EnsemblBacteriaiADC52251; ADC52251; BpOF4_21279.
ADC52252; ADC52252; BpOF4_21284.
KEGGibpf:BpOF4_21279.
bpf:BpOF4_21284.
PATRICi31950839. VBIBacPse80461_4084.

Keywords - Coding sequence diversityi

RNA suppression of termination

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP001879 Genomic DNA. Translation: ADC52251.1. Sequence problems.
CP001879 Genomic DNA. Translation: ADC52252.1. Different initiation.
Z14112 Genomic DNA. Translation: CAA78484.1. Sequence problems.
Z14112 Genomic DNA. Translation: CAA78485.1. Sequence problems.
PIRiS23866.
RefSeqiYP_003429143.1. NC_013792.1.
YP_003429144.1. NC_013792.1.

3D structure databases

ProteinModelPortaliP34184.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiADC52251; ADC52251; BpOF4_21279.
ADC52252; ADC52252; BpOF4_21284.
KEGGibpf:BpOF4_21279.
bpf:BpOF4_21284.
PATRICi31950839. VBIBacPse80461_4084.

Enzyme and pathway databases

BioCyciBPSE398511:GJI9-4279-MONOMER.
BPSE398511:GJI9-4280-MONOMER.

Family and domain databases

Gene3Di1.10.290.10. 1 hit.
1.10.460.10. 2 hits.
3.40.50.140. 1 hit.
InterProiIPR000380. Topo_IA.
IPR003601. Topo_IA_2.
IPR023406. Topo_IA_AS.
IPR013497. Topo_IA_cen.
IPR013824. Topo_IA_cen_sub1.
IPR013826. Topo_IA_cen_sub3.
IPR023405. Topo_IA_core_domain.
IPR003602. Topo_IA_DNA-bd_dom.
IPR013498. Topo_IA_Znf.
IPR025589. Toprim_C_rpt.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF13342. Toprim_Crpt. 1 hit.
PF01396. zf-C4_Topoisom. 1 hit.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Genome of alkaliphilic Bacillus pseudofirmus OF4 reveals adaptations that support the ability to grow in an external pH range from 7.5 to 11.4."
    Janto B., Ahmed A., Ito M., Liu J., Hicks D.B., Pagni S., Fackelmayer O.J., Smith T.A., Earl J., Elbourne L.D., Hassan K., Paulsen I.T., Kolsto A.B., Tourasse N.J., Ehrlich G.D., Boissy R., Ivey D.M., Li G.
    , Xue Y., Ma Y., Hu F.Z., Krulwich T.A.
    Environ. Microbiol. 13:3289-3309(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: OF4.
    Plasmid: pBpOF4-01
  2. "A 1.6 kb region of Bacillus firmus OF4 DNA encodes a homolog of Escherichia coli and yeast DNA topoisomerases and may contain a translational readthrough of UGA."
    Ivey D.M., Cheng J., Krulwich T.A.
    Nucleic Acids Res. 20:4928-4928(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 27-706.

Entry informationi

Entry nameiTOP1_BACPE
AccessioniPrimary (citable) accession number: P34184
Secondary accession number(s): D3G1M5, D3G1M6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1994
Last sequence update: January 11, 2011
Last modified: June 24, 2015
This is version 90 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

The sequence displayed is the result of a readthrough of the terminator UGA between codons for Tyr-288 and Leu-290. However, translational readthrough of UGA in this protein has not been proven.Curated

Keywords - Technical termi

Complete proteome, Plasmid, 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.