Information on EC 5.99.1.3 - DNA topoisomerase (ATP-hydrolysing)

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
5.99.1.3
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RECOMMENDED NAME
GeneOntology No.
DNA topoisomerase (ATP-hydrolysing)
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP-dependent breakage, passage and rejoining of double-stranded DNA
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isomerization
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SYSTEMATIC NAME
IUBMB Comments
DNA topoisomerase (ATP-hydrolysing)
The enzyme can introduce negative superhelical turns into double-stranded circular DNA. One unit has nicking-closing activity, and another catalyses super-twisting and hydrolysis of ATP (cf. EC 5.99.1.2 DNA topoisomerase).
CAS REGISTRY NUMBER
COMMENTARY hide
142805-56-9
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80449-01-0
formerly not distinguished from EC 5.99.1.2
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Manually annotated by BRENDA team
cauliflower
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
i.e. CVM-1
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Manually annotated by BRENDA team
Citrobacter spp.
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Manually annotated by BRENDA team
strain AB, gene can4
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Manually annotated by BRENDA team
Danio rerio TL/WIK
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
strain RFM443, gene gyrA encoding the A subunit
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Manually annotated by BRENDA team
Escherichia coli K-12 RFM443
strain RFM443, gene gyrA encoding the A subunit
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
Leishmania donovani MHOM/80/IN/Dd8
strain MHOM/80/IN/Dd8
SwissProt
Manually annotated by BRENDA team
Q8PUB7: subunit A, Q8PUB8: subunit B
Q8PUB7 and Q8PUB8
SwissProt
Manually annotated by BRENDA team
Q8PUB7: subunit A, Q8PUB8: subunit B
Q8PUB7 and Q8PUB8
SwissProt
Manually annotated by BRENDA team
encoded by 2 orfs TopoM and TopoN
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Manually annotated by BRENDA team
Paramecium bursaria chlorella virus
i.e. PBCV-1
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Manually annotated by BRENDA team
Paramecium bursaria Chlorella virus-1
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
chloroquine-sensitive and chloroquine-resistant strains
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
strains AC1679-1682
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Manually annotated by BRENDA team
strain PAO
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
strains CiproS and CiproR, and a methicillin-resistant strain
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Manually annotated by BRENDA team
wild-type and a methicillin-resistant strain
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Manually annotated by BRENDA team
wild-type strain and strain Pen I/R
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
Trypanosoma brucei Lister 427
clone 221a
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
metabolism
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mechanistically link of DNA topoisomerase IIbeta-dependent dsDNA breaks and the components of the DNA damage and repair machinery in regulated gene transcription
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
catenated DNA + ATP + H2O
minicircular DNA + ADP + phosphate
show the reaction diagram
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decatenation
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?
catenated kDNA + ATP + H2O
unlinked monomer kDNA + ADP + phosphate
show the reaction diagram
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?
closed circular DNA + ATP
positively supercoiled DNA + ADP + phosphate
show the reaction diagram
CVM-1 viral DNA + ATP + H2O
?
show the reaction diagram
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breakage, passage, decatenation, and rejoining of CVM-1 viral DNA, viral DNA contains 10% N6-methyladenine and 42% 5-methylcytosine, 4fold decreased activity compared to unmodified DNA
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?
DNA
?
show the reaction diagram
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the enzyme is capable of introducing positive supercoils into closed-circular DNA. It catalyzes positive supercoiling both in negatively supercoiled DNA and in relaxed DNA. The reactions require the presence of ATP
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?
DNA
positively supercoiled DNA
show the reaction diagram
positively supercoils DNA, the enzyme requires ATP, which is bound and hydrolysed by a helicase-like domain
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?
DNA + ATP
?
show the reaction diagram
DNA + ATP + H2O
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show the reaction diagram
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binding of the enzyme on double-stranded DNA alters the DNA structure in two ways: (I) reduction of the linking number in a circular duplex after covalent closure by a ligase; (II) singe-stranded DNA cleavage. Positive supercoiling of DNA in the presence of ATP. Catalyzes ATP-dependent positive supercoiling and its stoichiometric binding to DNA
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?
DNA + ATP + H2O
?
show the reaction diagram
DNA + ATP + H2O
DNA + ADP + phosphate
show the reaction diagram
double-stranded DNA + ATP + H2O
?
show the reaction diagram
double-stranded M13 DNA + ATP + H2O
?
show the reaction diagram
breakage, passage, and rejoining of double-stranded M13 DNA, including ATPase activity
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?
dsDNA + ATP + H2O
?
show the reaction diagram
form I DNA + ATP + H2O
form IV DNA + ADP + phosphate
show the reaction diagram
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?
four-way junction DNA + ATP + H2O
?
show the reaction diagram
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binds and cleaves four-way junction DNA in vitro, topoisomerase IIbeta has a 4fold higher affinity for the four-way junction than for the linear duplex, the enzyme binds to the centre of the duplex, the four-way junction contains the sequence of a 40 bp linear duplex (containing a single topoisomerase cleavage site) along to adjacent arms, with the cleavage site straddling the point of strand exchange, the remaining two arms are comprised of sequences which do not contain topoisomerase cleavage sites, except that a potential m-AMSA-inducible cleavage site is introduced across the junction of these two arms
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?
kDNA + ATP + H2O
?
show the reaction diagram
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decatenation
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?
kinetoplast DNA + ATP
?
show the reaction diagram
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decatenation
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?
kinetoplast DNA + ATP + H2O
?
show the reaction diagram
linear DNA fragments of viral SSV1 DNA + ATP + H2O
?
show the reaction diagram
negatively supercoiled DNA
positively supercoiled DNA
show the reaction diagram
the enzyme catalyzes a ATP-dependent DNA-positive supercoiling reaction of closed DNA plasmids. ATP is required for a correct coordination of DNA cleavage. The enzyme is able to induce positive supercoiling with ATP concentrations of 0.0001 mM. The efficiency of the reaction increases with increasing nucleotide concentrations, with an optimum between 0.1 and 1.0 mM. In the absence of ATP, the enzyme shows weak type I topoisomerase-like DNA relaxation activity. At all temperatures, relaxed and/or positive topoisomers are produced when a certain amount of the negative substrate is still present, thus suggesting that the enzyme is highly processive, i.e. it performs multiple supercoiling cycles before detaching from DNA and attacking a new substrate molecule. In the absence of ATP the enzyme shows weak type I topoisomerase-like DNA relaxation activity
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?
negatively supercoiled DNA + ATP + H2O
?
show the reaction diagram
negatively supercoiled DNA + ATP + H2O
highly positively supercolied DNA + ADP + phosphate
show the reaction diagram
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activity of TopR2 of is strictly dependent on the presence of ATP. The enzyme exhibits an high intrinsic processivity. It is able to introduce a very high number of positive superturns in DNA
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?
negatively supercoiled DNA + ATP + H2O
positively supercoil DNA + ADP + phosphate
show the reaction diagram
negatively supercoiled DNA + ATP + H2O
positively supercoiled DNA + ADP + phosphate
show the reaction diagram
negatively supercoiled pBR322 DNA
?
show the reaction diagram
negatively supercoiled pBR322 DNA + ATP + H2O
?
show the reaction diagram
negatively supercoiled pHOTI plasmid DNA + ATP + H2O
?
show the reaction diagram
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?
negatively supercoiled plasmid DNA + ATP + H2O
negatively supercoiled plasmid DNA + ADP + phosphate
show the reaction diagram
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the full-length recombinant enzyme sustains ATP-dependent positive supercoiling. The C-terminal half of Sulfolobus reverse gyrase, expressed in Escherichia coli, exhibits a topoisomerase I activity, independent of the presence of ATP and specific of negative supercoils.The N-terminal domain does not directly unwind DNA but acts more likely by driving ATP-dependent conformational changes within the whole enzyme, reminiscent of a protein motor
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?
network of DNA rings + ATP + H2O
monomer DNA circles + ADP + phosphate
show the reaction diagram
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?
network of DNA rings + ATP + H2O
monomeric DNA circles + ADP + phosphate
show the reaction diagram
PBCV-1 viral DNA + ATP + H2O
?
show the reaction diagram
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breakage, passage, decatenation, and rejoining of PBCV-1 viral DNA, viral DNA contains N6-methyladenine and 5-methylcytosine, decreased activity compared to unmodified DNA
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?
pBR322 DNA + ATP + H2O
?
show the reaction diagram
plasmid DNA + ATP + H2O
?
show the reaction diagram
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cleavage of plasmid DNA
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?
plasmid DNA pRYG + ATP + H2O
?
show the reaction diagram
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cleavage of plasmid DNA pRYG
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?
relaxed DNA + ATP + H2O
positively supercoiled DNA + ADP + phosphate
show the reaction diagram
relaxed pBR322 plasmid + ATP + H2O
supercoiled pBR322 plasmid + ADP + phosphate
show the reaction diagram
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supercoiling
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?
supercoiled DNA + ATP + H2O
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show the reaction diagram
substrate is supercoiled scpBR322 plasmid DNA. Topo2a creates transient breaks in supercoiled DNA in an ATP-dependent manner resulting in DNA relaxation
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supercoiled DNA + ATP + H2O
catenated DNA networks + ADP + phosphate
show the reaction diagram
supercoiled DNA + ATP + H2O
relaxed DNA + ADP + phosphate
show the reaction diagram
supercoiled dsDNA
?
show the reaction diagram
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relaxation of supercoiled dsDNA, reaction mechanism
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?
supercoiled pBR 322 plasmid DNA + ATP + H2O
relaxed pBR 322 plasmid DNA + ADP + phosphate
show the reaction diagram
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?
supercoiled pBR322 + ATP
?
show the reaction diagram
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relaxation
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?
supercoiled pBR322 DNA
?
show the reaction diagram
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cleavage of supercoiled pBR322 DNA
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?
supercoiled pBR322 DNA + ATP
?
show the reaction diagram
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relaxation
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?
supercoiled pBR322 plasmid + ATP + H2O
relaxed pBR322 plasmid + ADP + phosphate
show the reaction diagram
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relaxation
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?
supercoiled pKMp27 DNA + ATP + H2O
?
show the reaction diagram
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relaxation of supercoiled pKMp27 DNA
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?
supercoiled plasmid DNA + ATP + H2O
relaxed DNA + ADP + phosphate
show the reaction diagram
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?
supercoiled plasmid pBR322 DNA + ATP
?
show the reaction diagram
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relaxation of supercoiled DNA
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?
supercoiled pRYG DNA + ATP + H2O
?
show the reaction diagram
theta-174 phage DNA + ATP + H2O
?
show the reaction diagram
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unknotting of theta-174 phage DNA
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?
topoligically relaxed plasmid DNA + ATP
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show the reaction diagram
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catenation in preesence of a DNA crowding agent
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?
additional information
?
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