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P06612 (TOP1_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 152. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA topoisomerase 1

EC=5.99.1.2
Alternative name(s):
DNA topoisomerase I
Omega-protein
Relaxing enzyme
Swivelase
Untwisting enzyme
Gene names
Name:topA
Synonyms:supX
Ordered Locus Names:b1274, JW1266
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length865 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.8 Ref.9 Ref.15

Catalytic activity

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining. Ref.8 Ref.9 Ref.14 Ref.15

Cofactor

Magnesium. 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+ and Ca2+. Ref.9 Ref.15

Subunit structure

Monomer.

Sequence similarities

Belongs to the type IA topoisomerase family.

Contains 1 Toprim domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 865865DNA topoisomerase 1 HAMAP-Rule MF_00952
PRO_0000145147

Regions

Domain3 – 142140Toprim
Zinc finger599 – 63032C4-type 1 HAMAP-Rule MF_00952
Zinc finger662 – 68928C4-type 2 HAMAP-Rule MF_00952
Zinc finger711 – 73626C4-type 3 HAMAP-Rule MF_00952
Region192 – 1976Interaction with DNA HAMAP-Rule MF_00952

Sites

Active site3191O-(5'-phospho-DNA)-tyrosine intermediate Ref.8 Ref.10 Ref.15
Metal binding91Magnesium 1; catalytic By similarity
Metal binding1111Magnesium 1; catalytic Probable
Metal binding1111Magnesium 2 Probable
Metal binding1131Magnesium 2 Probable
Site331Interaction with DNA
Site1681Interaction with DNA
Site1691Interaction with DNA
Site1721Interaction with DNA
Site1771Interaction with DNA
Site1841Interaction with DNA
Site3211Interaction with DNA
Site5071Interaction with DNA

Experimental info

Mutagenesis91E → A: Abolishes enzyme activity. Ref.8
Mutagenesis91E → Q: No effect on DNA cleavage activity. Ref.8
Mutagenesis1111D → A: Abolishes both magnesium binding and enzyme activity; when associated with A-113 and A-115. Ref.9
Mutagenesis1131D → A: Abolishes both magnesium binding and enzyme activity; when associated with A-111 and A-115. Ref.9
Mutagenesis1151E → A: Abolishes both magnesium binding and enzyme activity; when associated with A-111 and A-113. Ref.9
Mutagenesis1681R → A: Abolishes enzyme activity. Ref.15
Mutagenesis1721D → A: Abolishes enzyme activity. Ref.15
Mutagenesis3191Y → A: Abolishes enzyme activity. Ref.8
Mutagenesis3211R → A: Abolishes enzyme activity. Ref.8
Mutagenesis3211R → K: No effect. Ref.8
Mutagenesis3651H → A: No effect. Ref.8 Ref.14
Mutagenesis3651H → R: Increases DNA binding affinity. Ref.8 Ref.14
Mutagenesis4961T → A: No effect. Ref.8
Sequence conflict7871P → R in AAA23641. Ref.6

Secondary structure

.......................................................................................................... 865
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P06612 [UniParc].

Last modified February 1, 1995. Version 2.
Checksum: 8C13F767FE5B178C

FASTA86597,350
        10         20         30         40         50         60 
MGKALVIVES PAKAKTINKY LGSDYVVKSS VGHIRDLPTS GSAAKKSADS TSTKTAKKPK 

        70         80         90        100        110        120 
KDERGALVNR MGVDPWHNWE AHYEVLPGKE KVVSELKQLA EKADHIYLAT DLDREGEAIA 

       130        140        150        160        170        180 
WHLREVIGGD DARYSRVVFN EITKNAIRQA FNKPGELNID RVNAQQARRF MDRVVGYMVS 

       190        200        210        220        230        240 
PLLWKKIARG LSAGRVQSVA VRLVVERERE IKAFVPEEFW EVDASTTTPS GEALALQVTH 

       250        260        270        280        290        300 
QNDKPFRPVN KEQTQAAVSL LEKARYSVLE REDKPTTSKP GAPFITSTLQ QAASTRLGFG 

       310        320        330        340        350        360 
VKKTMMMAQR LYEAGYITYM RTDSTNLSQD AVNMVRGYIS DNFGKKYLPE SPNQYASKEN 

       370        380        390        400        410        420 
SQEAHEAIRP SDVNVMAESL KDMEADAQKL YQLIWRQFVA CQMTPAKYDS TTLTVGAGDF 

       430        440        450        460        470        480 
RLKARGRILR FDGWTKVMPA LRKGDEDRIL PAVNKGDALT LVELTPAQHF TKPPARFSEA 

       490        500        510        520        530        540 
SLVKELEKRG IGRPSTYASI ISTIQDRGYV RVENRRFYAE KMGEIVTDRL EENFRELMNY 

       550        560        570        580        590        600 
DFTAQMENSL DQVANHEAEW KAVLDHFFSD FTQQLDKAEK DPEEGGMRPN QMVLTSIDCP 

       610        620        630        640        650        660 
TCGRKMGIRT ASTGVFLGCS GYALPPKERC KTTINLVPEN EVLNVLEGED AETNALRAKR 

       670        680        690        700        710        720 
RCPKCGTAMD SYLIDPKRKL HVCGNNPTCD GYEIEEGEFR IKGYDGPIVE CEKCGSEMHL 

       730        740        750        760        770        780 
KMGRFGKYMA CTNEECKNTR KILRNGEVAP PKEDPVPLPE LPCEKSDAYF VLRDGAAGVF 

       790        800        810        820        830        840 
LAANTFPKSR ETRAPLVEEL YRFRDRLPEK LRYLADAPQQ DPEGNKTMVR FSRKTKQQYV 

       850        860 
SSEKDGKATG WSAFYVDGKW VEGKK 

« Hide

References

« Hide 'large scale' references
[1]"Complete nucleotide sequence of the topA gene encoding Escherichia coli DNA topoisomerase I."
Tse-Dinh Y.-C., Wang J.C.
J. Mol. Biol. 191:321-331(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]Lynch D.A., Wang J.C.
Submitted (SEP-1991) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], SEQUENCE REVISION.
[3]"A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0-40.1 min region on the linkage map."
Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T., Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K., Miki T., Mizobuchi K., Mori H., Mori T., Motomura K. expand/collapse author list , Nakade S., Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G., Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y., Wada C., Yamamoto Y., Horiuchi T.
DNA Res. 3:363-377(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[5]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[6]"DNA sequences of the cysB regions of Salmonella typhimurium and Escherichia coli."
Ostrowski J., Jagura-Burdzy G., Kredich N.M.
J. Biol. Chem. 262:5999-6005(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 698-865.
[7]"Escherichia coli proteome analysis using the gene-protein database."
VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.
Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY 2D-GEL.
[8]"Identification of active site residues in Escherichia coli DNA topoisomerase I."
Chen S.J., Wang J.C.
J. Biol. Chem. 273:6050-6056(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF GLU-9; TYR-319; ARG-321; HIS-365 AND THR-496, CATALYTIC ACTIVITY, FUNCTION, ACTIVE SITE.
[9]"The acidic triad conserved in type IA DNA topoisomerases is required for binding of Mg(II) and subsequent conformational change."
Zhu C.X., Tse-Dinh Y.C.
J. Biol. Chem. 275:5318-5322(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF ASP-111; ASP-113 AND GLU-115, COFACTOR, FUNCTION, ENZYME MECHANISM, METAL-BINDING SITES, CATALYTIC ACTIVITY.
[10]"Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I."
Lima C.D., Wang J.C., Mondragon A.
Nature 367:138-146(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 1-597, PUTATIVE METAL-BINDING SITES, ACTIVE SITE.
[11]"Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I."
Yu L., Zhu C.-X., Tse-Dinh Y.-C., Fesik S.W.
Biochemistry 34:7622-7628(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 745-865.
[12]"Conformational changes in E. coli DNA topoisomerase I."
Feinberg H., Lima C.D., Mondragon A.
Nat. Struct. Biol. 6:918-922(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 214-477.
[13]"Protein-nucleotide interactions in E. coli DNA topoisomerase I."
Feinberg H., Changela A., Mondragon A.
Nat. Struct. Biol. 6:961-968(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 1-597 IN COMPLEXES WITH NUCLEOTIDES.
[14]"Structure of a complex between E. coli DNA topoisomerase I and single-stranded DNA."
Perry K., Mondragon A.
Structure 11:1349-1358(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.67 ANGSTROMS) OF 1-592 OF MUTANT ARG-365 IN COMPLEX WITH SINGLE-STANDED DNA, MUTAGENESIS OF HIS-365, CATALYTIC ACTIVITY.
[15]"Crystal structure of a covalent intermediate in DNA cleavage and rejoining by Escherichia coli DNA topoisomerase I."
Zhang Z., Cheng B., Tse-Dinh Y.C.
Proc. Natl. Acad. Sci. U.S.A. 108:6939-6944(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 1-596 OF MUTANT ASN-111 IN COMPLEX WITH DNA, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, COFACTOR, MUTAGENESIS OF ARG-168 AND ASP-172, DNA-BINDING SITES, ENZYME MECHANISM.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X04475 Genomic DNA. Translation: CAA28164.1.
M15041 Genomic DNA. Translation: AAA23641.1.
U00096 Genomic DNA. Translation: AAC74356.1.
AP009048 Genomic DNA. Translation: BAA14811.1.
PIRISECTP. E64875.
RefSeqNP_415790.1. NC_000913.3.
YP_489542.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
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-ray2.30A1-596[»]
ProteinModelPortalP06612.
SMRP06612. Positions 2-619, 745-865.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-11011N.
IntActP06612. 68 interactions.
MINTMINT-1218330.
STRING511145.b1274.

Proteomic databases

PaxDbP06612.
PRIDEP06612.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC74356; AAC74356; b1274.
BAA14811; BAA14811; BAA14811.
GeneID12930585.
945862.
KEGGecj:Y75_p1248.
eco:b1274.
PATRIC32117806. VBIEscCol129921_1323.

Organism-specific databases

EchoBASEEB1006.
EcoGeneEG11013. topA.

Phylogenomic databases

eggNOGCOG0551.
HOGENOMHOG000004018.
KOK03168.
OMAMVYKMGR.
OrthoDBEOG6S7XQ9.
PhylomeDBP06612.
ProtClustDBPRK07561.

Enzyme and pathway databases

BioCycEcoCyc:EG11013-MONOMER.
ECOL316407:JW1266-MONOMER.
MetaCyc:EG11013-MONOMER.

Gene expression databases

GenevestigatorP06612.

Family and domain databases

Gene3D1.10.460.10. 3 hits.
2.70.20.10. 2 hits.
3.40.50.140. 1 hit.
HAMAPMF_00952. Topoisom_1_prok.
InterProIPR000380. 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.
IPR013498. Topo_IA_Znf.
IPR005733. TopoI_bac-type.
IPR013263. TopoI_Znr_bac.
IPR028612. Topoisom_1_IA.
IPR006171. Toprim_domain.
[Graphical view]
PANTHERPTHR11390. PTHR11390. 1 hit.
PfamPF08272. Topo_Zn_Ribbon. 2 hits.
PF01131. Topoisom_bac. 1 hit.
PF01751. Toprim. 1 hit.
PF01396. zf-C4_Topoisom. 2 hits.
[Graphical view]
PRINTSPR00417. PRTPISMRASEI.
SMARTSM00437. TOP1Ac. 1 hit.
SM00436. TOP1Bc. 1 hit.
SM00493. TOPRIM. 1 hit.
[Graphical view]
SUPFAMSSF56712. SSF56712. 1 hit.
TIGRFAMsTIGR01051. topA_bact. 1 hit.
PROSITEPS00396. TOPOISOMERASE_I_PROK. 1 hit.
PS50880. TOPRIM. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP06612.
PROP06612.

Entry information

Entry nameTOP1_ECOLI
AccessionPrimary (citable) accession number: P06612
Entry history
Integrated into UniProtKB/Swiss-Prot: January 1, 1988
Last sequence update: February 1, 1995
Last modified: April 16, 2014
This is version 152 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene