Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

DNA topoisomerase 1

Gene

topA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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 annotation3 Publications

Catalytic activityi

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.UniRule annotation4 Publications

Cofactori

Mg2+2 Publications, Mn2+2 Publications, Ca2+2 PublicationsNote: Binds two Mg2+ ions per subunit. The magnesium ions form salt bridges with both the protein and the DNA. Can also accept other divalent metal cations, such as Mn2+ or Ca2+.2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi9Magnesium 1; catalyticUniRule annotation1
Metal bindingi111Magnesium 1; catalyticCurated1
Metal bindingi111Magnesium 2Curated1
Metal bindingi113Magnesium 2Curated1
Active sitei319O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation3 Publications1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri599 – 630C4-type 1Add BLAST32
Zinc fingeri662 – 689C4-type 2Add BLAST28
Zinc fingeri711 – 736C4-type 3Add BLAST26

GO - Molecular functioni

  • DNA binding Source: UniProtKB-KW
  • DNA topoisomerase activity Source: EcoCyc
  • DNA topoisomerase type I activity Source: EcoCyc
  • magnesium ion binding Source: UniProtKB-HAMAP

GO - Biological processi

  • DNA topological change Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Isomerase, Topoisomerase

Keywords - Ligandi

DNA-binding, Magnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG11013-MONOMER.
ECOL316407:JW1266-MONOMER.
MetaCyc:EG11013-MONOMER.
BRENDAi5.99.1.2. 2026.

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:supX
Ordered Locus Names:b1274, JW1266
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11013. topA.

Subcellular locationi

GO - Cellular componenti

  • chromosome Source: InterPro
  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi9E → A: Abolishes enzyme activity. 1 Publication1
Mutagenesisi9E → Q: No effect on DNA cleavage activity. 1 Publication1
Mutagenesisi111D → A: Abolishes both magnesium binding and enzyme activity; when associated with A-113 and A-115. 1 Publication1
Mutagenesisi113D → A: Abolishes both magnesium binding and enzyme activity; when associated with A-111 and A-115. 1 Publication1
Mutagenesisi115E → A: Abolishes both magnesium binding and enzyme activity; when associated with A-111 and A-113. 1 Publication1
Mutagenesisi168R → A: Abolishes enzyme activity. 1 Publication1
Mutagenesisi172D → A: Abolishes enzyme activity. 1 Publication1
Mutagenesisi319Y → A: Abolishes enzyme activity. 1 Publication1
Mutagenesisi321R → A: Abolishes enzyme activity. 1 Publication1
Mutagenesisi321R → K: No effect. 1 Publication1
Mutagenesisi365H → A: No effect. 2 Publications1
Mutagenesisi365H → R: Increases DNA binding affinity. 2 Publications1
Mutagenesisi496T → A: No effect. 1 Publication1

Chemistry databases

ChEMBLiCHEMBL3259513.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001451471 – 865DNA topoisomerase 1Add BLAST865

Proteomic databases

EPDiP06612.
PaxDbiP06612.
PRIDEiP06612.

Interactioni

Subunit structurei

Monomer.UniRule annotation2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei33Interaction with DNA1
Sitei168Interaction with DNA1
Sitei169Interaction with DNA1
Sitei172Interaction with DNA1
Sitei177Interaction with DNA1
Sitei184Interaction with DNA1
Sitei321Interaction with DNA1
Sitei507Interaction with DNA1

Protein-protein interaction databases

BioGridi4259579. 139 interactors.
DIPiDIP-11011N.
IntActiP06612. 68 interactors.
MINTiMINT-1218330.
STRINGi511145.b1274.

Structurei

Secondary structure

1865
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 9Combined sources6
Helixi11 – 18Combined sources8
Beta strandi25 – 29Combined sources5
Beta strandi35 – 37Combined sources3
Helixi64 – 71Combined sources8
Beta strandi72 – 74Combined sources3
Turni75 – 79Combined sources5
Turni87 – 89Combined sources3
Helixi90 – 101Combined sources12
Beta strandi104 – 108Combined sources5
Helixi114 – 127Combined sources14
Helixi131 – 133Combined sources3
Beta strandi134 – 136Combined sources3
Helixi144 – 152Combined sources9
Helixi159 – 186Combined sources28
Helixi197 – 213Combined sources17
Beta strandi218 – 227Combined sources10
Beta strandi229 – 231Combined sources3
Beta strandi233 – 241Combined sources9
Helixi251 – 263Combined sources13
Beta strandi266 – 278Combined sources13
Helixi286 – 297Combined sources12
Helixi301 – 313Combined sources13
Beta strandi316 – 318Combined sources3
Helixi329 – 342Combined sources14
Helixi345 – 347Combined sources3
Beta strandi356 – 358Combined sources3
Beta strandi362 – 364Combined sources3
Helixi377 – 379Combined sources3
Helixi385 – 401Combined sources17
Beta strandi406 – 417Combined sources12
Beta strandi420 – 431Combined sources12
Helixi433 – 437Combined sources5
Beta strandi458 – 470Combined sources13
Helixi479 – 488Combined sources10
Turni494 – 496Combined sources3
Helixi497 – 506Combined sources10
Beta strandi509 – 513Combined sources5
Beta strandi516 – 519Combined sources4
Helixi521 – 533Combined sources13
Helixi535 – 538Combined sources4
Helixi540 – 554Combined sources15
Helixi560 – 579Combined sources20
Helixi582 – 584Combined sources3
Beta strandi593 – 598Combined sources6
Beta strandi600 – 603Combined sources4
Beta strandi605 – 610Combined sources6
Beta strandi615 – 620Combined sources6
Helixi626 – 628Combined sources3
Beta strandi633 – 635Combined sources3
Helixi648 – 650Combined sources3
Helixi651 – 657Combined sources7
Turni663 – 665Combined sources3
Beta strandi668 – 675Combined sources8
Beta strandi678 – 683Combined sources6
Turni684 – 688Combined sources5
Beta strandi692 – 694Combined sources3
Turni702 – 705Combined sources4
Beta strandi712 – 714Combined sources3
Beta strandi717 – 722Combined sources6
Beta strandi724 – 733Combined sources10
Beta strandi740 – 742Combined sources3
Helixi744 – 746Combined sources3
Beta strandi756 – 762Combined sources7
Beta strandi764 – 767Combined sources4
Beta strandi769 – 775Combined sources7
Beta strandi778 – 785Combined sources8
Turni786 – 788Combined sources3
Helixi797 – 802Combined sources6
Turni803 – 806Combined sources4
Helixi809 – 811Combined sources3
Helixi812 – 815Combined sources4
Beta strandi826 – 829Combined sources4
Turni833 – 835Combined sources3
Beta strandi840 – 843Combined sources4
Beta strandi851 – 855Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1CY0X-ray2.45A1-597[»]
1CY1X-ray2.30A1-597[»]
1CY2X-ray2.30A1-597[»]
1CY4X-ray2.55A1-597[»]
1CY6X-ray2.50A1-597[»]
1CY7X-ray2.40A1-597[»]
1CY8X-ray2.45A1-597[»]
1CY9X-ray1.80A/B214-477[»]
1CYYX-ray2.15A/B214-477[»]
1ECLX-ray1.90A1-597[»]
1MW8X-ray1.90X1-592[»]
1MW9X-ray1.67X1-592[»]
1YUANMR-A745-865[»]
3PWTX-ray1.90A1-596[»]
3PX7X-ray2.30A1-595[»]
4RULX-ray2.90A2-865[»]
ProteinModelPortaliP06612.
SMRiP06612.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP06612.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 142ToprimUniRule annotationAdd BLAST140

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni192 – 197Interaction with DNA6

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 fingeri599 – 630C4-type 1Add BLAST32
Zinc fingeri662 – 689C4-type 2Add BLAST28
Zinc fingeri711 – 736C4-type 3Add BLAST26

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
COG0551. LUCA.
HOGENOMiHOG000004018.
InParanoidiP06612.
KOiK03168.
OMAiVVECDKC.
PhylomeDBiP06612.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 3 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.
IPR013263. TopoI_Znr_bac.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 2 hits.
PfamiPF08272. Topo_Zn_Ribbon. 2 hits.
PF01131. 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. 1 hit.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P06612-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MGKALVIVES PAKAKTINKY LGSDYVVKSS VGHIRDLPTS GSAAKKSADS
60 70 80 90 100
TSTKTAKKPK KDERGALVNR MGVDPWHNWE AHYEVLPGKE KVVSELKQLA
110 120 130 140 150
EKADHIYLAT DLDREGEAIA WHLREVIGGD DARYSRVVFN EITKNAIRQA
160 170 180 190 200
FNKPGELNID RVNAQQARRF MDRVVGYMVS PLLWKKIARG LSAGRVQSVA
210 220 230 240 250
VRLVVERERE IKAFVPEEFW EVDASTTTPS GEALALQVTH QNDKPFRPVN
260 270 280 290 300
KEQTQAAVSL LEKARYSVLE REDKPTTSKP GAPFITSTLQ QAASTRLGFG
310 320 330 340 350
VKKTMMMAQR LYEAGYITYM RTDSTNLSQD AVNMVRGYIS DNFGKKYLPE
360 370 380 390 400
SPNQYASKEN SQEAHEAIRP SDVNVMAESL KDMEADAQKL YQLIWRQFVA
410 420 430 440 450
CQMTPAKYDS TTLTVGAGDF RLKARGRILR FDGWTKVMPA LRKGDEDRIL
460 470 480 490 500
PAVNKGDALT LVELTPAQHF TKPPARFSEA SLVKELEKRG IGRPSTYASI
510 520 530 540 550
ISTIQDRGYV RVENRRFYAE KMGEIVTDRL EENFRELMNY DFTAQMENSL
560 570 580 590 600
DQVANHEAEW KAVLDHFFSD FTQQLDKAEK DPEEGGMRPN QMVLTSIDCP
610 620 630 640 650
TCGRKMGIRT ASTGVFLGCS GYALPPKERC KTTINLVPEN EVLNVLEGED
660 670 680 690 700
AETNALRAKR RCPKCGTAMD SYLIDPKRKL HVCGNNPTCD GYEIEEGEFR
710 720 730 740 750
IKGYDGPIVE CEKCGSEMHL KMGRFGKYMA CTNEECKNTR KILRNGEVAP
760 770 780 790 800
PKEDPVPLPE LPCEKSDAYF VLRDGAAGVF LAANTFPKSR ETRAPLVEEL
810 820 830 840 850
YRFRDRLPEK LRYLADAPQQ DPEGNKTMVR FSRKTKQQYV SSEKDGKATG
860
WSAFYVDGKW VEGKK
Length:865
Mass (Da):97,350
Last modified:February 1, 1995 - v2
Checksum:i8C13F767FE5B178C
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti787P → R in AAA23641 (PubMed:3032952).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04475 Genomic DNA. Translation: CAA28164.1.
M15041 Genomic DNA. Translation: AAA23641.1.
U00096 Genomic DNA. Translation: AAC74356.1.
AP009048 Genomic DNA. Translation: BAA14811.1.
PIRiE64875. ISECTP.
RefSeqiNP_415790.1. NC_000913.3.
WP_001297122.1. NZ_CP014272.1.

Genome annotation databases

EnsemblBacteriaiAAC74356; AAC74356; b1274.
BAA14811; BAA14811; BAA14811.
GeneIDi945862.
KEGGiecj:JW1266.
eco:b1274.
PATRICi32117806. VBIEscCol129921_1323.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X04475 Genomic DNA. Translation: CAA28164.1.
M15041 Genomic DNA. Translation: AAA23641.1.
U00096 Genomic DNA. Translation: AAC74356.1.
AP009048 Genomic DNA. Translation: BAA14811.1.
PIRiE64875. ISECTP.
RefSeqiNP_415790.1. NC_000913.3.
WP_001297122.1. NZ_CP014272.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1CY0X-ray2.45A1-597[»]
1CY1X-ray2.30A1-597[»]
1CY2X-ray2.30A1-597[»]
1CY4X-ray2.55A1-597[»]
1CY6X-ray2.50A1-597[»]
1CY7X-ray2.40A1-597[»]
1CY8X-ray2.45A1-597[»]
1CY9X-ray1.80A/B214-477[»]
1CYYX-ray2.15A/B214-477[»]
1ECLX-ray1.90A1-597[»]
1MW8X-ray1.90X1-592[»]
1MW9X-ray1.67X1-592[»]
1YUANMR-A745-865[»]
3PWTX-ray1.90A1-596[»]
3PX7X-ray2.30A1-595[»]
4RULX-ray2.90A2-865[»]
ProteinModelPortaliP06612.
SMRiP06612.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259579. 139 interactors.
DIPiDIP-11011N.
IntActiP06612. 68 interactors.
MINTiMINT-1218330.
STRINGi511145.b1274.

Chemistry databases

ChEMBLiCHEMBL3259513.

Proteomic databases

EPDiP06612.
PaxDbiP06612.
PRIDEiP06612.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74356; AAC74356; b1274.
BAA14811; BAA14811; BAA14811.
GeneIDi945862.
KEGGiecj:JW1266.
eco:b1274.
PATRICi32117806. VBIEscCol129921_1323.

Organism-specific databases

EchoBASEiEB1006.
EcoGeneiEG11013. topA.

Phylogenomic databases

eggNOGiENOG4105C73. Bacteria.
COG0550. LUCA.
COG0551. LUCA.
HOGENOMiHOG000004018.
InParanoidiP06612.
KOiK03168.
OMAiVVECDKC.
PhylomeDBiP06612.

Enzyme and pathway databases

BioCyciEcoCyc:EG11013-MONOMER.
ECOL316407:JW1266-MONOMER.
MetaCyc:EG11013-MONOMER.
BRENDAi5.99.1.2. 2026.

Miscellaneous databases

EvolutionaryTraceiP06612.
PROiP06612.

Family and domain databases

CDDicd00186. TOP1Ac. 1 hit.
Gene3Di1.10.460.10. 3 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.
IPR013263. TopoI_Znr_bac.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERiPTHR11390. PTHR11390. 2 hits.
PfamiPF08272. Topo_Zn_Ribbon. 2 hits.
PF01131. 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. 1 hit.
TIGRFAMsiTIGR01051. topA_bact. 1 hit.
PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiTOP1_ECOLI
AccessioniPrimary (citable) accession number: P06612
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: February 1, 1995
Last modified: November 2, 2016
This is version 173 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.