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Information on EC 5.6.2.2 - DNA topoisomerase (ATP-hydrolysing) and Organism(s) Saccharolobus shibatae and UniProt Accession O05207
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5.6.2.2 DNA topoisomerase (ATP-hydrolysing)IUBMB Comments
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 5.6.2.1 DNA topoisomerase).
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- 5.6.2.2
- myosin
- na+
- adp
- sarcoplasmic
- cardiac
- actin
- etoposide
- helicase
- chromatin
- strand
- triphosphatase
- ouabain
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multidrug
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supercoiling
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electrogenic
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The taxonomic range for the selected organisms is: Saccharolobus shibatae
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
atpase, topoisomerase ii, dna gyrase, topo ii, gyrase, top2a, dna topoisomerase ii, topoisomerase iialpha, topo iialpha, topoisomerase ii alpha, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
DNA gyrase
-
-
-
-
DNA topoisomerase II
-
-
-
-
DNA topoisomerase type II
-
-
-
-
DNA topoisomerase VI
Isomerase, deoxyribonucleate topo-, II
-
-
-
-
NP170 proteins
-
-
-
-
Nuclear proteins 170,000-mol.wt.
-
-
-
-
Protein Gp39
-
-
-
-
Protein Gp52
-
-
-
-
Protein Gp60
-
-
-
-
Proteins , NP170 (specific proteins and subclasses nuclear protein, 170,000-mol.-wt.)
-
-
-
-
PsTopII
-
-
-
-
topo VI
TOPOII
-
-
-
-
Topoisomerase II
-
-
-
-
Topoisomerase type II
-
-
-
-
Type II-DNA-topoisomerase
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
isomerization
-
-
-
-
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 5.6.2.1 DNA topoisomerase).
CAS REGISTRY NUMBER
COMMENTARY
142805-56-9
-
80449-01-0
formerly not distinguished from EC 5.99.1.2
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
catenated DNA + ATP + H2O
minicircular DNA + ADP + phosphate
decatenation
-
-
?
DNA + ATP
?
DNA topoisomerase VI relaxes both negatively and positively supercoiled DNA in the presence of ATP and has no DNA supercoiling activity
-
-
?
double-stranded DNA + ATP + H2O
?
the enzyme generates ATP-dependent double-strand breaks with two-nucleotide overhangs on supercoiled or linear DNA. topoVI is covalently attached to the 5'-ends of the broken DNA
-
-
?
linear DNA fragments of viral SSV1 DNA + ATP + H2O
?
-
ATP hydrolysis is necessary for DNA resealing
-
-
?
relaxed pBR322 plasmid + ATP + H2O
supercoiled pBR322 plasmid + ADP + phosphate
supercoiling
-
-
?
supercoiled DNA + ATP + H2O
catenated DNA networks + ADP + phosphate
-
catenation
-
?
supercoiled pBR322 plasmid + ATP + H2O
relaxed pBR322 plasmid + ADP + phosphate
relaxation
-
-
?
additional information
?
-
-
changes the linking number of a closed circular molecule by an increment of two
-
-
?
DNA + ATP + H2O
?
the enzyme helps disentangle chromosomes to facilitate cell division
-
-
?
DNA + ATP + H2O
?
-
the enzyme catalyzes an ATP-dependent positive DNA supercoiling reaction in vitro
-
-
?
DNA + ATP + H2O
?
the enzyme helps disentangle chromosomes to facilitate cell division. ATP binding elicits a major structural reorganization that is propagated to the DNA-cleavage center of the enzyme, explaining how ATP is coupled to DNA capture and strand scission
-
-
?
network of DNA rings + ATP + H2O
monomeric DNA circles + ADP + phosphate
-
decatenation
-
?
network of DNA rings + ATP + H2O
monomeric DNA circles + ADP + phosphate
-
enzyme is more efficient in decatenation than relaxation
-
?
supercoiled DNA + ATP + H2O
relaxed DNA + ADP + phosphate
-
relaxation
-
?
supercoiled DNA + ATP + H2O
relaxed DNA + ADP + phosphate
-
ATP-dependent relaxation of negative and positive supercoils
-
?
supercoiled DNA + ATP + H2O
relaxed DNA + ADP + phosphate
-
DNA cleavage by topo VI generates two-nucleotide 5'-protruding ends
-
-
?
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
DNA + ATP + H2O
?
the enzyme helps disentangle chromosomes to facilitate cell division
-
-
?
double-stranded DNA + ATP + H2O
?
the enzyme generates ATP-dependent double-strand breaks with two-nucleotide overhangs on supercoiled or linear DNA. topoVI is covalently attached to the 5'-ends of the broken DNA
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ATP
the formation of the double-strand breaks on supercoiled or linear DNA is strictly dependent on the presence of ATP or adenosine 5'-(beta,gamma-imino)triphosphate. ATP binding is required to stabilize an enzyme conformation able to cleave the DNA backbone
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
-
Mg2+ is effective in the concentration range 1-40 mM, optimal concentration is around 30 mM
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(1S,3S)-3-acetyl-3,5,12-trihydroxy-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside
-
-
radicicol
inhibits the decatenation and relaxation activities
additional information
geldanamycin does not inhibit the decatenation and relaxation activities
-
additional information
-
geldanamycin does not inhibit the decatenation and relaxation activities
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
single-strand binding-protein
-
from the archaeon Sulfolobus solfataricus. Stimulates all the steps of the reverse gyrase reaction: binding to DNA, DNA cleavage, strand passage and ligation. It also stimulates reverse gyrase positive supercoiling activity on DNA templates associated with the chromatin protein Sul7d
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
the enzyme helps disentangle chromosomes to facilitate cell division
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
45055
2 * 45055 (subunit A) + 2 * 60528 (subunit B), calculated from sequence
47000
60000
60528
2 * 45055 (subunit A) + 2 * 60528 (subunit B), calculated from sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
heterotetramer
tetramer
heterotetramer
2 * 45055 (subunit A) + 2 * 60528 (subunit B), calculated from sequence
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
structure of the ATP-binding subunit of topoisomerase VI in two states: an unliganded monomer and a nucleotide-bound dimer
hanging drop vapour diffusion method, in complex with the radicicol inhibitor
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
S424C
cysteine substitution mutant capable of forming an intersubunit disulfide bond upon ATP-induced dimerization. The mutant protein has a smaller radius of gyration (Rg) than the apoprotein.
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
65
-
pH 7, enzyme concentration 90 ng/ml, less than 15% loss of activity after 40 min
80
-
pH 7, enzyme concentration 90 ng/ml, half-life: about 35 min. At an enzyme concentration of 900 ng/ml less than 20% loss of activity after 40 min
95
-
pH 7, enzyme concentration 90 ng/ml, more than 90% inactivation after 5 min
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, 50 mM potassium phosphate buffer, 1 mM EDTA, 1 mM DTT, 0.0005% Triton X-100
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni2+ affinity column chromatography and heparin column chromatography
-
purification of the two recombinant subunits of Sulfolobus shibatae Topo IV from Escherichia coli
purification procedure of a fully soluble recombinant topoVI is developed by expressing both subunits simultaneously in Escherichia coli
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene structure, transcription unit and comparative sequence analysis with two other known reverse gyrases
overexpression in Escherichia coli. The A subunit exhibits clusters of arginines encoded by rare codons in Escherichia coli. The expression of this protein requires the coexpression of the minor Escherichia coli arginyl tRNA which reads AGG and AGA codons. The A subunit expressed in Escherichia coli is obtained from inclusion bodies after denaturation and renaturation. The B subunit is overexpressed in Escherichia coli and purified in soluble form. When purified B subunit is added to the renatured A subunit, ATP-dependent relaxation and decatenation activities of the hyperthermophilic DNA topoisomerase are reconstituted. The reconstituted recombinant enzyme exhibits a specific activity similar to the enzyme purified from Sulfolobus shibatae. It catalyzes transient double-strain cleavage of DNA and becomes covalently attached to the ends of the cleaved DNA
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Bergerat, A.; Gadelle, D.; Forterre, P.
Purification of a DNA topoisomerase II from the hyperthermophilic archaeon Sulfolobus shibatae
J. Biol. Chem.
269
27663-27669
1994
Saccharolobus shibatae
Buhler, C.; Gadelle, D.; Forterre, P.; Wang, J.C.; Bergerat, A.
Reconstitution of DNA topoisomerase VI of the thermophilic archaeon Sulfolobus shibatae from subunits separately overexpressed in Escherichia coli
Nucleic Acids Res.
26
5157-5162
1998
Saccharolobus shibatae (O05208 and O05207), Saccharolobus shibatae
Graille, M.; Cladiere, L.; Durand, D.; Lecointe, F.; Gadelle, D.; Quevillon-Cheruel, S.; Vachette, P.; Forterre, P.; van Tilbeurgh, H.
Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms
Structure
16
360-370
2008
Saccharolobus shibatae
Corbett, K.D.; Berger, J.M.
Structure of the topoisomerase VI-B subunit: implications for type II topoisomerase mechanism and evolution
EMBO J.
22
151-163
2003
Saccharolobus shibatae (O05207)
Jaxel, C.; Duguet, M.; Nadal, M.
Analysis of DNA cleavage by reverse gyrase from Sulfolobus shibatae B12
Eur. J. Biochem.
260
103-111
2006
Saccharolobus shibatae, Saccharolobus shibatae B12
Buhler, C.; Lebbink, J.H.; Bocs, C.; Ladenstein, R.; Forterre, P.
DNA topoisomerase VI generates ATP-dependent double-strand breaks with two-nucleotide overhangs
J. Biol. Chem.
276
37215-37222
2001
Saccharolobus shibatae (O05207 and O05208)
Corbett, K.D.; Benedetti, P.; Berger, J.M.
Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI
Nat. Struct. Mol. Biol.
14
611-609
2007
Saccharolobus shibatae (O05208 and O05207), Methanosarcina mazei (Q8PUB7 and Q8PUB8), Methanosarcina mazei DSM 3647 (Q8PUB7 and Q8PUB8)
Bergerat, A.; de Massy, B.; Gadelle, D.; Varoutas, P.C.; Nicolas, A.; Forterre, P.
An atypical topoisomerase II from Archaea with implications for meiotic recombination
Nature
386
414-417
1997
Saccharolobus shibatae (O05208 and O05207), Saccharolobus shibatae
Jaxel, C.; Bouthier, de la Tour, C.; Duguet, M.; Nadal, M.
Reverse gyrase gene from Sulfolobus shibatae B12: gene structure, transcription unit and comparative sequence analysis of the two domains
Nucleic Acids Res.
24
4668-4675
1996
Saccharolobus shibatae (P74759), Saccharolobus shibatae B12 (P74759)
Gadelle, D.; Bocs, C.; Graille, M.; Forterre, P.
Inhibition of archaeal growth and DNA topoisomerase VI activities by the Hsp90 inhibitor radicicol
Nucleic Acids Res.
33
2310-2317
2005
Saccharolobus shibatae (O05207 and O05208), Saccharolobus shibatae
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