P06612 · TOP1_ECOLI
- ProteinDNA topoisomerase 1
- GenetopA
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids865 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
Function
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.
Catalytic activity
Cofactor
Ca2+ (UniProtKB | Rhea| CHEBI:29108 )
Note: 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+.
Biotechnology
Has been used to construct a 2,4,6-trinitrotoluene (TNT) biosensor strain.
Features
Showing features for binding site, site, active site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 9 | Mg2+ (UniProtKB | ChEBI); catalytic | ||||
Sequence: E | ||||||
Site | 33 | Interaction with DNA | ||||
Sequence: H | ||||||
Binding site | 111 | Mg2+ (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Site | 168 | Interaction with DNA | ||||
Sequence: R | ||||||
Site | 169 | Interaction with DNA | ||||
Sequence: R | ||||||
Site | 172 | Interaction with DNA | ||||
Sequence: D | ||||||
Site | 177 | Interaction with DNA | ||||
Sequence: Y | ||||||
Site | 184 | Interaction with DNA | ||||
Sequence: W | ||||||
Active site | 319 | O-(5'-phospho-DNA)-tyrosine intermediate | ||||
Sequence: Y | ||||||
Site | 321 | Interaction with DNA | ||||
Sequence: R | ||||||
Site | 507 | Interaction with DNA | ||||
Sequence: R |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | chromosome | |
Cellular Component | cytosol | |
Molecular Function | DNA binding | |
Molecular Function | DNA topoisomerase activity | |
Molecular Function | DNA topoisomerase type I (single strand cut, ATP-independent) activity | |
Molecular Function | metal ion binding | |
Biological Process | DNA topological change |
Keywords
- Molecular function
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameDNA topoisomerase 1
- EC number
- Alternative names
Gene names
Organism names
- Organism
- Strains
- Taxonomic lineageBacteria > Pseudomonadota > Gammaproteobacteria > Enterobacterales > Enterobacteriaceae > Escherichia
Accessions
- Primary accessionP06612
Proteomes
Subcellular Location
UniProt Annotation
GO Annotation
Phenotypes & Variants
Features
Showing features for mutagenesis.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 9 | Abolishes enzyme activity. | ||||
Sequence: E → A | ||||||
Mutagenesis | 9 | No effect on DNA cleavage activity. | ||||
Sequence: E → Q | ||||||
Mutagenesis | 111 | Abolishes both magnesium binding and enzyme activity; when associated with A-113 and A-115. | ||||
Sequence: D → A | ||||||
Mutagenesis | 113 | Abolishes both magnesium binding and enzyme activity; when associated with A-111 and A-115. | ||||
Sequence: D → A | ||||||
Mutagenesis | 115 | Abolishes both magnesium binding and enzyme activity; when associated with A-111 and A-113. | ||||
Sequence: E → A | ||||||
Mutagenesis | 168 | Abolishes enzyme activity. | ||||
Sequence: R → A | ||||||
Mutagenesis | 172 | Abolishes enzyme activity. | ||||
Sequence: D → A | ||||||
Mutagenesis | 319 | Abolishes enzyme activity. | ||||
Sequence: Y → A | ||||||
Mutagenesis | 321 | Abolishes enzyme activity. | ||||
Sequence: R → A | ||||||
Mutagenesis | 321 | No effect. | ||||
Sequence: R → K | ||||||
Mutagenesis | 365 | No effect. | ||||
Sequence: H → A | ||||||
Mutagenesis | 365 | Increases DNA binding affinity. | ||||
Sequence: H → R | ||||||
Mutagenesis | 496 | No effect. | ||||
Sequence: T → A |
Chemistry
PTM/Processing
Features
Showing features for chain.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000145147 | 1-865 | DNA topoisomerase 1 | |||
Sequence: MGKALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEITKNAIRQAFNKPGELNIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQLDKAEKDPEEGGMRPNQMVLTSIDCPTCGRKMGIRTASTGVFLGCSGYALPPKERCKTTINLVPENEVLNVLEGEDAETNALRAKRRCPKCGTAMDSYLIDPKRKLHVCGNNPTCDGYEIEEGEFRIKGYDGPIVECEKCGSEMHLKMGRFGKYMACTNEECKNTRKILRNGEVAPPKEDPVPLPELPCEKSDAYFVLRDGAAGVFLAANTFPKSRETRAPLVEELYRFRDRLPEKLRYLADAPQQDPEGNKTMVRFSRKTKQQYVSSEKDGKATGWSAFYVDGKWVEGKK |
Proteomic databases
Expression
Induction
Transcription is increased specifically in response to 2,4,6-trinitrotoluene (TNT) and its indicator compounds 1,3-DNB, 2,4-DNT, and 2,6-DNT.
Interaction
Subunit
Monomer.
Binary interactions
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | P06612 | yigZ P27862 | 3 | EBI-544172, EBI-561235 |
Protein-protein interaction databases
Chemistry
Structure
Family & Domains
Features
Showing features for domain, region, compositional bias, zinc finger.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 3-142 | Toprim | ||||
Sequence: KALVIVESPAKAKTINKYLGSDYVVKSSVGHIRDLPTSGSAAKKSADSTSTKTAKKPKKDERGALVNRMGVDPWHNWEAHYEVLPGKEKVVSELKQLAEKADHIYLATDLDREGEAIAWHLREVIGGDDARYSRVVFNEI | ||||||
Region | 37-65 | Disordered | ||||
Sequence: LPTSGSAAKKSADSTSTKTAKKPKKDERG | ||||||
Compositional bias | 51-65 | Basic and acidic residues | ||||
Sequence: TSTKTAKKPKKDERG | ||||||
Domain | 158-575 | Topo IA-type catalytic | ||||
Sequence: NIDRVNAQQARRFMDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEFWEVDASTTTPSGEALALQVTHQNDKPFRPVNKEQTQAAVSLLEKARYSVLEREDKPTTSKPGAPFITSTLQQAASTRLGFGVKKTMMMAQRLYEAGYITYMRTDSTNLSQDAVNMVRGYISDNFGKKYLPESPNQYASKENSQEAHEAIRPSDVNVMAESLKDMEADAQKLYQLIWRQFVACQMTPAKYDSTTLTVGAGDFRLKARGRILRFDGWTKVMPALRKGDEDRILPAVNKGDALTLVELTPAQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEENFRELMNYDFTAQMENSLDQVANHEAEWKAVLDHFFSDFTQQL | ||||||
Region | 192-197 | Interaction with DNA | ||||
Sequence: SAGRVQ | ||||||
Zinc finger | 599-630 | C4-type 1 | ||||
Sequence: CPTCGRKMGIRTASTGVFLGCSGYALPPKERC | ||||||
Zinc finger | 662-689 | C4-type 2 | ||||
Sequence: CPKCGTAMDSYLIDPKRKLHVCGNNPTC | ||||||
Zinc finger | 711-736 | C4-type 3 | ||||
Sequence: CEKCGSEMHLKMGRFGKYMACTNEEC |
Sequence similarities
Belongs to the type IA topoisomerase family.
Keywords
- Domain
Phylogenomic databases
Family and domain databases
Sequence
- Sequence statusComplete
- Length865
- Mass (Da)97,350
- Last updated1995-02-01 v2
- Checksum8C13F767FE5B178C
Features
Showing features for compositional bias, sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 51-65 | Basic and acidic residues | ||||
Sequence: TSTKTAKKPKKDERG | ||||||
Sequence conflict | 787 | in Ref. 6; AAA23641 | ||||
Sequence: P → R |
Keywords
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
X04475 EMBL· GenBank· DDBJ | CAA28164.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
M15041 EMBL· GenBank· DDBJ | AAA23641.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
U00096 EMBL· GenBank· DDBJ | AAC74356.1 EMBL· GenBank· DDBJ | Genomic DNA | ||
AP009048 EMBL· GenBank· DDBJ | BAA14811.1 EMBL· GenBank· DDBJ | Genomic DNA |