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Protein

DNA topoisomerase 1

Gene

topA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

  • DNA topological change Source: EcoliWiki

Keywordsi

Molecular functionDNA-binding, Isomerase, Topoisomerase
LigandMagnesium, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciEcoCyc:EG11013-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

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
DrugBankiDB01812 Adenosine-3'-5'-Diphosphate
DB01643 Thymidine-5'-Phosphate

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

Binary interactionsi

WithEntry#Exp.IntActNotes
yigZP278623EBI-544172,EBI-561235

Protein-protein interaction databases

BioGridi4259579, 153 interactors
DIPiDIP-11011N
IntActiP06612, 69 interactors
STRINGi316385.ECDH10B_1389

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

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

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
OMAiPECKYTR
PhylomeDBiP06612

Family and domain databases

CDDicd00186 TOP1Ac, 1 hit
cd03363 TOPRIM_TopoIA_TopoI, 1 hit
Gene3Di1.10.290.10, 1 hit
1.10.460.10, 2 hits
2.70.20.10, 2 hits
HAMAPiMF_00952 Topoisom_1_prok, 1 hit
InterProiView protein in InterPro
IPR000380 Topo_IA
IPR003601 Topo_IA_2
IPR023406 Topo_IA_AS
IPR013497 Topo_IA_cen
IPR013824 Topo_IA_cen_sub1
IPR013825 Topo_IA_cen_sub2
IPR013826 Topo_IA_cen_sub3
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
IPR034149 TOPRIM_TopoI
PANTHERiPTHR42785 PTHR42785, 1 hit
PfamiView protein in Pfam
PF08272 Topo_Zn_Ribbon, 2 hits
PF01131 Topoisom_bac, 1 hit
PF01751 Toprim, 1 hit
PF01396 zf-C4_Topoisom, 2 hits
PRINTSiPR00417 PRTPISMRASEI
SMARTiView protein in SMART
SM00437 TOP1Ac, 1 hit
SM00436 TOP1Bc, 1 hit
SM00493 TOPRIM, 1 hit
SUPFAMiSSF56712 SSF56712, 1 hit
TIGRFAMsiTIGR01051 topA_bact, 1 hit
PROSITEiView protein in PROSITE
PS00396 TOPOISOMERASE_I_PROK, 1 hit
PS50880 TOPRIM, 1 hit

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
PATRICifig|1411691.4.peg.1010

Similar proteinsi

Entry informationi

Entry nameiTOP1_ECOLI
AccessioniPrimary (citable) accession number: P06612
Entry historyiIntegrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: February 1, 1995
Last modified: March 28, 2018
This is version 184 of the entry and version 2 of the sequence. See 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

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