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Protein

DNA topoisomerase 1

Gene

topA

Organism
Synechocystis sp. (strain PCC 6803 / Kazusa)
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 annotationNote: Binds two Mg2+ per subunit.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi8 – 81Magnesium 1; catalyticUniRule annotation
Sitei32 – 321Interaction with DNAUniRule annotation
Metal bindingi95 – 951Magnesium 1; catalyticUniRule annotation
Metal bindingi95 – 951Magnesium 2UniRule annotation
Metal bindingi97 – 971Magnesium 2UniRule annotation
Sitei151 – 1511Interaction with DNAUniRule annotation
Sitei152 – 1521Interaction with DNAUniRule annotation
Sitei155 – 1551Interaction with DNAUniRule annotation
Sitei160 – 1601Interaction with DNAUniRule annotation
Sitei167 – 1671Interaction with DNAUniRule annotation
Active sitei320 – 3201O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
Sitei322 – 3221Interaction with DNAUniRule annotation
Sitei515 – 5151Interaction with DNAUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding

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
Ordered Locus Names:slr2058
OrganismiSynechocystis sp. (strain PCC 6803 / Kazusa)
Taxonomic identifieri1111708 [NCBI]
Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechocystis
ProteomesiUP000001425 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 898898DNA topoisomerase 1PRO_0000145168Add
BLAST

Proteomic databases

PaxDbiP73810.

Interactioni

Subunit structurei

Monomer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliP73810.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini2 – 126125ToprimUniRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni175 – 1806Interaction with DNAUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiCOG1754.
HOGENOMiHOG000004020.
InParanoidiP73810.
KOiK03168.
OMAiTKRNPGP.
OrthoDBiEOG6S7XQ9.
PhylomeDBiP73810.

Family and domain databases

Gene3Di1.10.460.10. 2 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.
IPR005733. TopoI_bac-type.
IPR028612. Topoisom_1_IA.
IPR025589. Toprim_C_rpt.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF13368. Toprim_C_rpt. 3 hits.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P73810-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSKLVIVESP TKARTIRNYL PQDYRVEASM GHVRDLPASA EEVPAAYKDK
60 70 80 90 100
SWANLGVNVE DHFSPLYVIP KSKKKVVKEL QTALKNADEV ILATDEDREG
110 120 130 140 150
ESISWHLLQL LQPKVPIKRM VFHEITQEAI RSALENCRDI DENLVHAQET
160 170 180 190 200
RRILDRLVGY TLSPLLWKKI AWGLSAGRVQ SVAVRLIVQR ERARRAFKTA
210 220 230 240 250
GYWDLKAELE QNKNPFQAKL MTLGGTKLAN GSDFDPNTGA LLPDKQVVVL
260 270 280 290 300
DEAQAIALKE RLTGKPWAVV NTEEKPGVRK PSPPFTTSTL QQEANRKLGI
310 320 330 340 350
SARDTMRVAQ KLYEEGYITY MRTDSVHLSD QAVTAARNCV QQMYGKEYLS
360 370 380 390 400
PQPKQYTTKS KGAQEAHEAI RPAGTEFRIP NQTGLKDREL ALYELIWKRT
410 420 430 440 450
VACQMADARI TQLSVLLKVE DAEFRAAGKR IDFPGYFRAY VEGSDDPDAA
460 470 480 490 500
LENQEVILPP LKVGDRPNCR EIDTVGHETQ PPARYTEASL VKTLESEGVG
510 520 530 540 550
RPSTYASIIG TIIDRGYVQM RSKALTPTFT AFAVVSLLES HFPDLVDTGF
560 570 580 590 600
TSRMEQKLDE IAIGKTQWLP YLQGFFLGES GLENQVKVRQ DQIDPAIAKA
610 620 630 640 650
IELENLAAKV KIGKFGPYIE IPQGEEIITA SIPQDLTPAD LNPEQVAVLL
660 670 680 690 700
KQKTEGPDKV GIHPETGEPI FILIGAYGPY VQLGEATEEN KKPKRTSLPK
710 720 730 740 750
GVKPEDVTLE MAVGLLALPR NLGEHPESGK NIKASLGRFG PYVVHDQGKD
760 770 780 790 800
GKDYRSLKGD DDVLTITLER ALELLAEPKR GRGSRTPLKQ LGLHPEDQEP
810 820 830 840 850
VNLFKGPYGV YIKHGKVNAS LPEGETEETI TLEKALPLLA EKAGSGKKTS
860 870 880 890
RKKATTTAKG TKKTTSKKAS ATGTAKKTTT KRTTRKKAAS PDQSSEAG
Length:898
Mass (Da):99,340
Last modified:February 1, 1997 - v1
Checksum:i9416665977398EB3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000022 Genomic DNA. Translation: BAA17864.1.
PIRiS74903.

Genome annotation databases

EnsemblBacteriaiBAA17864; BAA17864; BAA17864.
KEGGisyy:SYNGTS_1288.
syz:MYO_113000.
PATRICi23839689. VBISynSp132158_1406.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000022 Genomic DNA. Translation: BAA17864.1.
PIRiS74903.

3D structure databases

ProteinModelPortaliP73810.
ModBaseiSearch...
MobiDBiSearch...

Proteomic databases

PaxDbiP73810.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAA17864; BAA17864; BAA17864.
KEGGisyy:SYNGTS_1288.
syz:MYO_113000.
PATRICi23839689. VBISynSp132158_1406.

Phylogenomic databases

eggNOGiCOG1754.
HOGENOMiHOG000004020.
InParanoidiP73810.
KOiK03168.
OMAiTKRNPGP.
OrthoDBiEOG6S7XQ9.
PhylomeDBiP73810.

Family and domain databases

Gene3Di1.10.460.10. 2 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.
IPR005733. TopoI_bac-type.
IPR028612. Topoisom_1_IA.
IPR025589. Toprim_C_rpt.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 1 hit.
PfamiPF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF13368. Toprim_C_rpt. 3 hits.
[Graphical view]
PRINTSiPR00417. PRTPISMRASEI.
SMARTiSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMiSSF56712. SSF56712. 1 hit.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions."
    Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T., Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.
    , Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.
    DNA Res. 3:109-136(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: PCC 6803 / Kazusa.

Entry informationi

Entry nameiTOP1_SYNY3
AccessioniPrimary (citable) accession number: P73810
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: February 1, 1997
Last modified: July 22, 2015
This is version 109 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. SIMILARITY comments
    Index of protein domains and families
  2. Synechocystis PCC 6803
    Synechocystis (strain PCC 6803): entries and gene names

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.