Any feedback?
Information on EC 5.6.2.1 - DNA topoisomerase and Organism(s) Mycobacterium tuberculosis and UniProt Accession P9WG49
for references in articles please use BRENDA:EC5.6.2.1Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
5.6.2.1 DNA topoisomeraseIUBMB Comments
These enzymes bring about the conversion of one topological isomer of DNA into another, e.g., the relaxation of superhelical turns in DNA, the interconversion of simple and knotted rings of single-stranded DNA, and the intertwisting of single-stranded rings of complementary sequences, cf. EC 5.6.2.2 DNA topoisomerase (ATP-hydrolysing).
Specify your search results
Word Map
- 5.6.2.1
- camptothecins
-
supercoiled
- strand
- etoposide
-
poison
- topotecan
- irinotecan
- leukemia
- chromatin
-
cleavable
- doxorubicin
-
single-stranded
- fluoroquinolones
-
quinolone
- ovarian
- duplex
- colorectal
- ciprofloxacin
-
ii-mediated
- fork
- helicase
-
schedule
- cisplatin
-
decatenation
-
antiproliferative
-
checkpoint
-
superhelical
- novobiocin
-
intercalation
-
breakage
-
dna-damaging
-
unwind
- neutropenia
-
dose-limiting
-
s-phase
- anthracyclines
-
cross-resistance
-
myelosuppression
- kinetoplast
-
taxanes
- levofloxacin
-
nalidixic
- mitoxantrone
- scleroderma
-
rejoin
- analysis
- chk1
- medicine
- drug development
- aphidicolin
-
etoposide-induced
- pharmacology
-
holliday
- diagnostics
- norfloxacin
The taxonomic range for the selected organisms is: Mycobacterium tuberculosis
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
Synonyms
topoisomerase, topoisomerase i, topo i, dna topoisomerase i, topoisomerase iv, dna topoisomerase, topoisomerase 1, human topoisomerase i, reverse gyrase, topoisomerase-i, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Deoxiribonucleate topoisomerase
-
-
-
-
Deoxiribonucleic topoisomerase
-
-
-
-
DNA topoisomerase I
Isomerase, deoxiribonucleate topo-
-
-
-
-
Late protein H6
-
-
-
-
Nicking-closing enzyme
-
-
-
-
omega-Protein
-
-
-
-
Relaxing enzyme
-
-
-
-
Reverse gyrase
-
-
-
-
Swivelase
-
-
-
-
TOP1mt
-
-
-
-
Topo I
-
-
-
-
Topoisomerase
-
-
-
-
Topoisomerase I
TpI
-
-
-
-
Type I DNA topoisomerase
-
-
-
-
Untwisting enzyme
-
-
-
-
Topoisomerase I
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
isomerization
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
DNA topoisomerase
These enzymes bring about the conversion of one topological isomer of DNA into another, e.g., the relaxation of superhelical turns in DNA, the interconversion of simple and knotted rings of single-stranded DNA, and the intertwisting of single-stranded rings of complementary sequences, cf. EC 5.6.2.2 DNA topoisomerase (ATP-hydrolysing).
CAS REGISTRY NUMBER
COMMENTARY
80449-01-0
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
supercoiled pBAD/Thio plasmid DNA
relaxced pBAD/Thio plasmid DNA
-
-
-
-
?
supercoiled DNA
relaxed closed circular DNA
-
negatively supercoiled DNA
-
?
additional information
?
-
the mycobacterial topoisomerase I physically interacts with its ribokinase both in vitro and in vivo with opposite effects on their respective function, overview. Interaction analysis, overview
-
-
?
additional information
?
-
-
the mycobacterial topoisomerase I physically interacts with its ribokinase both in vitro and in vivo with opposite effects on their respective function, overview. Interaction analysis, overview
-
-
?
additional information
?
-
substrate is supercoiled plasmid DNA
-
-
?
additional information
?
-
-
substrate is supercoiled plasmid DNA
-
-
?
additional information
?
-
-
mapping cleavage sites on single-stranded DNA substrate Mtop with length of 216 bases amplified from topA gene of Mycobacterium tuberculosis, substrate is negatively supercoiled DNA
-
-
?
additional information
?
-
-
topoisomerase I shows a negative interplay between MazF protein Rv1495. Through its C-terminal domain, MtbTopA physically interacts with and inhibits the mRNA cleavage activity of Rv1495, overview. Rv1495, in turn, inhibits the DNA cleavage activity of MtbTopA as well as its function of relaxation of supercoiled DNA
-
-
?
additional information
?
-
-
structure-function analysis of MtTOP1, overview
-
-
?
additional information
?
-
enzyme activity on relaxation of supercoiled pUC18 DNA or on 5' end labeled oligonucleotides having the strong topoisomerase I site, the enzyme cleaves DNA at preferred sites in a pattern similar to its ortholog from Mycobacterium smegmatis
-
-
?
additional information
?
-
-
enzyme activity on relaxation of supercoiled pUC18 DNA or on 5' end labeled oligonucleotides having the strong topoisomerase I site, the enzyme cleaves DNA at preferred sites in a pattern similar to its ortholog from Mycobacterium smegmatis
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
the mycobacterial topoisomerase I physically interacts with its ribokinase both in vitro and in vivo with opposite effects on their respective function, overview. Interaction analysis, overview
-
-
?
additional information
?
-
-
the mycobacterial topoisomerase I physically interacts with its ribokinase both in vitro and in vivo with opposite effects on their respective function, overview. Interaction analysis, overview
-
-
?
additional information
?
-
-
topoisomerase I shows a negative interplay between MazF protein Rv1495. Through its C-terminal domain, MtbTopA physically interacts with and inhibits the mRNA cleavage activity of Rv1495, overview. Rv1495, in turn, inhibits the DNA cleavage activity of MtbTopA as well as its function of relaxation of supercoiled DNA
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
-
required for DNA substrate relaxation, optimal at 5-12.5 mM
Mg2+
-
the DNA cleavage activity of MtTOP1-G116 S is Mg2+-dependent
Mg2+
required, acidic residues D111 and E115 are involved in Mg2+ coordination
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Rv2436
inhibits the TopA activity on supercoiled DNA. The ribokinase, encoded by gene Rv2436, acts as a netaive regulator of TopA activity
-
Rv1495
-
inhibits the DNA cleavage activity of MtbTopA as well as its function of relaxation of supercoiled DNA. An N-terminus fragment of Rv1495, designated Rv1495-N(29-56), lost mRNA cleavage activity, but retained a significant physical interaction and inhibitory effect on TopA proteins, overview. No DNA-binding activity is seen with Rv1495, even at a high protein concentration
-
additional information
oligonucleotides containing the specific recognition sequence inhibit the activity of the enzyme, as well as the monoclonal antibody 2F3G4, developed against MstopoI inhibited the relaxation activity of the enzyme. No inhibition with non-specific oligonucleotides
-
additional information
-
oligonucleotides containing the specific recognition sequence inhibit the activity of the enzyme, as well as the monoclonal antibody 2F3G4, developed against MstopoI inhibited the relaxation activity of the enzyme. No inhibition with non-specific oligonucleotides
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
the mycobacterial topoisomerase I physically interacts with its ribokinase both in vitro and in vivo with opposite effects on their respective function, overview. While the interaction between the two proteins inhibits the ability of TopA to relax supercoiled DNA, it stimulates ribokinase activity as a regulatory strategy for efficient utilization of D-ribose
malfunction
-
accumulation of cleavage complex formed by inactivated MtTOP1 is lethal for the cell
additional information
-
the TOPRIM motif DxDxxG is strictly conserved in type IA topoisomerase sequences and plays an essential role for divalent ion coordination and cleavage-religation of DNA during catalysis
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
structure-function analysis of MtTOP1, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
sitting drop vapor diffusion method, using 0.2 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5, and 25% (w/v) PEG3350
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D111A
site-directed mutagenesis, mutation of the Mg2+-binding residue affects DNA relaxation activity, mutant D111A is dependent on Mg2+ for DNA cleavage and is compromised in religation
D111N
-
site-directed mutagenesis, the mutation is lethal for the host
E115A
site-directed mutagenesis, mutation of the Mg2+-binding residue affects DNA relaxation activity, the mutant is compromised in religation
G116S
-
site-directed mutagenesis, MtTOP1 TOPRIM motif mutation, the mutation inhibits DNA religation. The DNA cleavage activity of MtTOP1-G116 S is Mg2+-dependent
H139C
-
site-directed mutagenesis, the mutant can be labeled with fluorophores with no significant loss of relaxation activity, the mutant complements the temperature sensitive topA function of Escherichia coli strain AS17
K524C
-
site-directed mutagenesis, the mutant can be labeled with fluorophores with no significant loss of relaxation activity, the mutant complements the temperature sensitive topA function of Escherichia coli strain AS17
L170C
-
site-directed mutagenesis, the mutant can be labeled with fluorophores with no significant loss of relaxation activity, the mutant complements the temperature sensitive topA function of Escherichia coli strain AS17
T142C
-
site-directed mutagenesis, the mutant can be labeled with fluorophores with no significant loss of relaxation activity, the mutant complements the temperature sensitive topA function of Escherichia coli strain AS17
Y174C
-
site-directed mutagenesis, the mutant can be labeled with fluorophores with no significant loss of relaxation activity, the mutant complements the temperature sensitive topA function of Escherichia coli strain AS17
additional information
additional information
the His6 tagged-MtbTopA protein is immobilized on an NTA chip. When an increasing amount of GST tagged-Rv2436 protein pass over the chip, they cause a substantial response, overview
additional information
-
the His6 tagged-MtbTopA protein is immobilized on an NTA chip. When an increasing amount of GST tagged-Rv2436 protein pass over the chip, they cause a substantial response, overview
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
His6-tagged recombinant enzyme from Escherichia coli strain BL21 (DE3) by nickel affinity chromatography, cleavage and elimination of the His-tag
-
Ni Sepharose 6 column chromatography and single-stranded DNA cellulose column chromatography
-
recombinant nontagged enzyme from Escherichia coli strain BL21 by ammonium sulfate fractionation, dialysis, and heparin affinity chromatography, recombinant wild-type and mutant His-tagged enzymes from Escherichia coli strain BL21(DE3) by ammonium sulfate fractionation, dialysis, and nickel affinity chromatography, native enzyme from Mycobacterium tuberculosis strain H37Ra
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene MtbTopA, co-expression with gene Rv2436, encoding a ribokinase of Mycobacterium tuberculosis, in Escherichia coli strain BL21. Interaction analysis using the two-hybrid system
expression of the soluble His6-tagged enzyme in Escherichia coli strain BL21 (DE3)
-
overexpression of wild-type and mutant His-tagged and non-tagged enzymes in Escherichia coli strain BL21(DE3)
plasmid-encoded recombinant MtTOP1 can complement the temperature sensitive topA function of Escherichia coli strain AS17 for growth at 42°C. The relaxation activity of recombinant wild-type MtTOP1 is functional in Escherichia coli. No complementation from the Y342A or G116S MtTOP1 mutants, but by mutant H139C, L170C, Y174C, T142C, and K524C. Overexpression of MtTOP1 mutant G116S leads to accumulation of cleavage complex formed by MtTOP1 in Escherichia coli
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
-
the absence of cysteine residues in MtTOP1 makes it an attractive system for introduction of potentially informative chemical or spectroscopic probes at specific positions via cysteine mutagenesis. Such probes could be useful for development of high throughput screening assays and can be utilized for fluorescence probe incorporation and fluorescence resonance energy transfer measurement with fluorophore-labeled oligonucleotide substrate
drug development
-
the enzyme is an attractive target for discovery of novel tuberculosis drugs that act by enhancing the accumulation of the topoisomerase-DNA cleavage product
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Yang, F.; Lu, G.; Rubin, H.
Cloning, expression, purification and characterization of DNA topoisomerase I of Mycobacterium tuberculosis
Gene
178
63-69
1996
Mycobacterium tuberculosis, Mycobacterium tuberculosis Erdman
Annamalai, T.; Dani, N.; Cheng, B.; Tse-Dinh, Y.C.
Analysis of DNA relaxation and cleavage activities of recombinant Mycobacterium tuberculosis DNA topoisomerase I from a new expression and purification protocol
BMC Biochem.
10
18
2009
Escherichia coli, Mycobacterium tuberculosis
Yang, Q.; Liu, Y.; Huang, F.; He, Z.G.
Physical and functional interaction between D-ribokinase and topoisomerase I has opposite effects on their respective activity in Mycobacterium smegmatis and Mycobacterium tuberculosis
Arch. Biochem. Biophys.
512
135-142
2011
Mycolicibacterium smegmatis, Mycobacterium tuberculosis (P9WG49), Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv (P9WG49)
Narula, G.; Becker, J.; Cheng, B.; Dani, N.; Abrenica, M.V.; Tse-Dinh, Y.C.
The DNA relaxation activity and covalent complex accumulation of Mycobacterium tuberculosis topoisomerase I can be assayed in Escherichia coli: application for identification of potential FRET-dye labeling sites
BMC Biochem.
11
41
2010
Mycobacterium tuberculosis
Huang, F.; He, Z.G.
Characterization of an interplay between a Mycobacterium tuberculosis MazF homolog, Rv1495 and its sole DNA topoisomerase I
Nucleic Acids Res.
38
8219-8230
2010
Mycobacterium tuberculosis, Mycolicibacterium smegmatis
Godbole, A.A.; Leelaram, M.N.; Bhat, A.G.; Jain, P.; Nagaraja, V.
Characterization of DNA topoisomerase I from Mycobacterium tuberculosis: DNA cleavage and religation properties and inhibition of its activity
Arch. Biochem. Biophys.
528
197-203
2012
Mycobacterium tuberculosis (A5U8X0), Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Ra / ATCC 25177 (A5U8X0)
EXTERNAL LINKS (specific for EC-Number 5.6.2.1)
Transporter Classification Database (TCDB): 3.A.7.7.1
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2023.1 (January 2023)
Legal
Curated at
Member of
