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Protein

DNA topoisomerase 1

Gene

topA

Organism
Treponema pallidum (strain Nichols)
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)DescriptionActionsGraphical viewLength
Metal bindingi23Magnesium 1; catalyticUniRule annotation1
Metal bindingi96Magnesium 1; catalyticUniRule annotation1
Metal bindingi96Magnesium 2UniRule annotation1
Metal bindingi98Magnesium 2UniRule annotation1
Active sitei312O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri591 – 617C4-type 1Add BLAST27
Zinc fingeri628 – 657C4-type 2Add BLAST30
Zinc fingeri670 – 696C4-type 3Add BLAST27

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

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:TP_0394
OrganismiTreponema pallidum (strain Nichols)
Taxonomic identifieri243276 [NCBI]
Taxonomic lineageiBacteriaSpirochaetesSpirochaetalesSpirochaetaceaeTreponema
Proteomesi
  • UP000000811 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001451701 – 731DNA topoisomerase 1Add BLAST731

Interactioni

Subunit structurei

Monomer.UniRule annotation

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei47Interaction with DNAUniRule annotation1
Sitei154Interaction with DNAUniRule annotation1
Sitei155Interaction with DNAUniRule annotation1
Sitei158Interaction with DNAUniRule annotation1
Sitei163Interaction with DNAUniRule annotation1
Sitei170Interaction with DNAUniRule annotation1
Sitei314Interaction with DNAUniRule annotation1
Sitei501Interaction with DNAUniRule annotation1

Protein-protein interaction databases

IntActiO83409. 2 interactors.
STRINGi243276.TP0394.

Structurei

3D structure databases

ProteinModelPortaliO83409.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini17 – 130ToprimUniRule annotationAdd BLAST114

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni178 – 183Interaction with DNAUniRule annotation6

Sequence similaritiesi

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

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri591 – 617C4-type 1Add BLAST27
Zinc fingeri628 – 657C4-type 2Add BLAST30
Zinc fingeri670 – 696C4-type 3Add BLAST27

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
COG0551. LUCA.
KOiK03168.
OMAiVVECDKC.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok. 1 hit.
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. 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.

O83409-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEVRGLQPKR QKTFARKHLV IVESPAKAQT IEKYLGTQYV VRASMGHVID
60 70 80 90 100
LPKSRLAIDI EHDFQPEYIT VRGRAQCLKE LRTLSKQSLQ VFLASDRDRE
110 120 130 140 150
GEAIAYHLAQ SIQAYCDTPI KRIVFNEITP HAIRAAIGHP VPIDTAKVNA
160 170 180 190 200
QKARRVLDRL VGYHLCPLLW HKVKNGLSAG RVQSVALRLI CEREVEVKRF
210 220 230 240 250
VPEEYWTVEG TFEKDKKSFS ALLILIQGKK AVFKSKQEAT SAIGLFSQSE
260 270 280 290 300
ARVSQIRSFE KNVRPKQPFT TSTLQQCAAN RLGFTSRKTM QVAQQLYEGV
310 320 330 340 350
SLGTHRVGLI TYMRTDSVRV SEAAVKEVRA WIATHFSDAL PGTPNRYAAK
360 370 380 390 400
GKSQDAHEAI RPTYVAHTPE RIKAHLTRDQ IRLYTLIWER FVASQMTDAR
410 420 430 440 450
VRSLTFEITA GPAVFSATET QVIEQGFYRV LKMLSPKDLS KAVLPPTKEG
460 470 480 490 500
EVVALHNVQS VQHFTQGPVR YTDASIVKML EEKGIGRPST YAPTISVLLD
510 520 530 540 550
RYYVTRIQKQ LMPTPLGKVI SDLLTTYFHD VVDVSFTARM ESKLDEVEED
560 570 580 590 600
KIKWNCVIAD FYPAFSEKVS TVMKDLNSMR GVFDEKTDVV CSQCGDTMVK
610 620 630 640 650
KLGRFGFFLA CGKFPECRNT QPVPLAKCPR PACDGNIVGK KTRGRKEFYG
660 670 680 690 700
CTRFPVCDFV THFKPTFAVC PQCRCFLVEK SNRRVGTYTA CVNPECRYVS
710 720 730
PTRKNLSLGK EAVLDGSHRG AQDKGAVQHY E
Length:731
Mass (Da):82,441
Last modified:November 1, 1998 - v1
Checksum:iC0F0C6C3DDD16F29
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000520 Genomic DNA. Translation: AAC65378.1.
PIRiD71332.
RefSeqiWP_010881842.1. NC_021490.2.

Genome annotation databases

EnsemblBacteriaiAAC65378; AAC65378; TP_0394.
GeneIDi2610767.
KEGGitpa:TP_0394.
PATRICi20530797. VBITrePal57110_0418.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000520 Genomic DNA. Translation: AAC65378.1.
PIRiD71332.
RefSeqiWP_010881842.1. NC_021490.2.

3D structure databases

ProteinModelPortaliO83409.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiO83409. 2 interactors.
STRINGi243276.TP0394.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC65378; AAC65378; TP_0394.
GeneIDi2610767.
KEGGitpa:TP_0394.
PATRICi20530797. VBITrePal57110_0418.

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
COG0551. LUCA.
KOiK03168.
OMAiVVECDKC.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 2 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPiMF_00952. Topoisom_1_prok. 1 hit.
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. 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...

Entry informationi

Entry nameiTOP1_TREPA
AccessioniPrimary (citable) accession number: O83409
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: November 1, 1998
Last modified: November 2, 2016
This is version 118 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

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 one 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.