Releases the supercoiling and torsional tension of DNA 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 than 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 (By similarity). Possesses negatively supercoiled DNA relaxing activity. Homo sapiens (taxid: 9606) EC: 5EC: .EC: 9EC: 9EC: .EC: 1EC: .EC: 2
>sp|Q9Z321|TOP3B_MOUSE DNA topoisomerase 3-beta-1 OS=Mus musculus GN=Top3b PE=2 SV=1
Releases the supercoiling and torsional tension of DNA 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 than 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 (By similarity). Possesses negatively supercoiled DNA relaxing activity.
Mus musculus (taxid: 10090)
EC: 5
EC: .
EC: 9
EC: 9
EC: .
EC: 1
EC: .
EC: 2
>sp|O96651|TOP3B_DROME DNA topoisomerase 3-beta OS=Drosophila melanogaster GN=Top3beta PE=2 SV=2
Releases the supercoiling and torsional tension of DNA 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 than 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 (By similarity). Weakly relaxes negative supercoils and displays a distinct preference for binding single-stranded DNA.
Releases the supercoiling and torsional tension of DNA 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 than 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 (By similarity). Essential for proper chromosome segregation in both meiosis and mitosis. Weakly relaxes negative supercoils and displays a distinct preference for binding single-stranded DNA. The TOP3-SGS1 protein complex may function as a eukaryotic reverse gyrase introducing positive supercoils into extrachromosomal ribosomal DNA rings.
Releases the supercoiling and torsional tension of DNA 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 than 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.
Score = 53.9 bits (128), Expect = 3e-07, Method: Composition-based stats.
Identities = 23/49 (46%), Positives = 29/49 (59%)
Query: 9 LKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLL 57
L+ Q + L +ISYGPCQ PTLGF V+R ++ F PE YW L
Sbjct: 190 LQTIQLQKSFDILQNKIISYGPCQFPTLGFVVDRWQRVEDFVPETYWHL 238
Releases the supercoiling and torsional tension of DNA 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 than 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.
Releases the supercoiling and torsional tension of DNA 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 than 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 (By similarity). Weakly relaxes negative supercoils and displays a distinct preference for binding single-stranded DNA.
Score = 49.7 bits (117), Expect = 6e-06, Method: Composition-based stats.
Identities = 20/49 (40%), Positives = 32/49 (65%)
Query: 19 GDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGEW 67
G L S +S G QTPTL V+R +I++F+PE YW + +T + +G++
Sbjct: 186 GRLGKSFLSAGRVQTPTLAIVVDREREIQSFRPERYWTISITFDKDGQF 234
Releases the supercoiling and torsional tension of DNA 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 than 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.
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 19/42 (45%), Positives = 29/42 (69%)
Query: 25 LISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGE 66
++S G Q PTL F VER +I++F P+PYW++ L + NG+
Sbjct: 194 VLSTGRVQGPTLKFLVEREREIQSFVPKPYWVIKLVIEKNGQ 235
Releases the supercoiling and torsional tension of DNA 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 than 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.
Score = 46.6 bits (109), Expect = 4e-05, Method: Composition-based stats.
Identities = 19/42 (45%), Positives = 27/42 (64%)
Query: 25 LISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGE 66
++S G Q PTL F VER +I++F P PYW++ L NG+
Sbjct: 194 VLSTGRVQGPTLKFLVEREREIQSFVPRPYWVIKLIFEKNGQ 235
Releases the supercoiling and torsional tension of DNA 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 than 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.
Score = 61.4 bits (150), Expect = 1e-14
Identities = 18/35 (51%), Positives = 23/35 (65%)
Query: 21 LDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYW 55
L ++S G QTPTLG VER +I+ F P+PYW
Sbjct: 54 LRNGVLSAGRVQTPTLGLIVEREREIKNFVPKPYW 88
Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit. Length = 89
>gnl|CDD|238110 cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases
Score = 63.8 bits (156), Expect = 6e-14
Identities = 16/34 (47%), Positives = 22/34 (64%)
Query: 24 SLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLL 57
++S G Q+PTLG VER +I+ F PE YW +
Sbjct: 33 GVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEI 66
Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand. Length = 381
>gnl|CDD|216317 pfam01131, Topoisom_bac, DNA topoisomerase
This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA. Length = 365
>gnl|CDD|235971 PRK07219, PRK07219, DNA topoisomerase I; Validated
Score = 55.7 bits (135), Expect = 4e-11
Identities = 15/42 (35%), Positives = 20/42 (47%)
Query: 21 LDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLN 62
L ++S G Q+P L VER +I F PE YW +
Sbjct: 162 LKRGVLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFE 203
Length = 570
>gnl|CDD|184936 PRK14973, PRK14973, DNA topoisomerase I; Provisional
Score = 47.5 bits (113), Expect = 3e-08
Identities = 19/40 (47%), Positives = 24/40 (60%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65
+S G Q PTL F VER +I F P+PYW++ TL G
Sbjct: 187 LSAGRVQGPTLAFLVEREREINLFVPKPYWVIKATLEKGG 226
This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent [DNA metabolism, DNA replication, recombination, and repair]. Length = 618
>gnl|CDD|235602 PRK05776, PRK05776, DNA topoisomerase I; Provisional
Score = 38.5 bits (90), Expect = 6e-05
Identities = 15/40 (37%), Positives = 20/40 (50%)
Query: 27 SYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGE 66
S G Q+ L V+R +I+ F PE YW +D T E
Sbjct: 159 SAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQKGEE 198
This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events [DNA metabolism, DNA replication, recombination, and repair]. Length = 610
>gnl|CDD|233252 TIGR01056, topB, DNA topoisomerase III, bacteria and conjugative plasmid
This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent [DNA metabolism, DNA replication, recombination, and repair]. Length = 660
>gnl|CDD|181555 PRK08780, PRK08780, DNA topoisomerase I; Provisional
This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases
Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Type IA topoisomerases are comprised of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA: an N-terminal alpha/beta Toprim domain, domain 2 and the C-terminal domain 4 are winged-helix domains, and domain 3 is a beta-barrel. Domains 1 (Toprim) and 3 form the active site of the enzyme, while the winged helix domains 2 and 4 form a single-strand DNA-binding groove [, ]. This entry represents the central portion of the enzyme, which covers domains 2 and 3 in topoisomerase type IA enzymes. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1CYY_A 3PWT_A 1CY4_A 1CY9_A 1ECL_A 1CY7_A 1CY8_A 1CY6_A 1MW8_X 1CY0_A ....
Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase I, 67K N-terminal domain
species: Escherichia coli [TaxId: 562]
Score = 41.0 bits (95), Expect = 2e-06
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 26 ISYGPCQTPTLGFCVERHDKIRTFKPEPYW 55
+S G Q+ + VER +I+ F PE +W
Sbjct: 190 LSAGRVQSVAVRLVVEREREIKAFVPEEFW 219
class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase III
species: Escherichia coli [TaxId: 562]
Score = 31.9 bits (71), Expect = 0.003
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 25 LISYGPCQTPTLGFCVERHDKIRTFKPEPYW 55
++S G QTP LG V R ++I F + ++
Sbjct: 192 VLSVGRVQTPVLGLVVRRDEEIENFVAKDFF 222
class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase I, 67K N-terminal domain
species: Escherichia coli [TaxId: 562]
class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: DNA topoisomerase III
species: Escherichia coli [TaxId: 562]
class: Multi-domain proteins (alpha and beta)
fold: Prokaryotic type I DNA topoisomerase
superfamily: Prokaryotic type I DNA topoisomerase
family: Prokaryotic type I DNA topoisomerase
domain: Topoisomerase "domain" of reverse gyrase
species: Archaeon Archaeoglobus fulgidus [TaxId: 2234]
