G3DSA:3.40.50.670

G3DSA:3.40.50.670

CATH-Gene3D entry
Member databaseCATH-Gene3D
CATH-Gene3D typehomologous superfamily

Description
Imported from IPR013759

DNA topoisomerases regulate the number of topological links between two DNA strands (i.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
[1]
. 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
[3, 7]
. DNA topoisomerases are divided into two classes: type I enzymes (
5.6.2.2
; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (
5.6.2.2
; topoisomerases II, IV and VI) break double-strand DNA
[4]
.

Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils
[2]
.

Type IIA topoisomerases together manage chromosome integrity and topology in cells. Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively; this topoisomerase II forms a homodimer that is equivalent to the bacterial heterotetramer. There are four functional domains in topoisomerase II: domain 1 (N-terminal of gyrB) is an ATPase, domain 2 (C-terminal of gyrB) is responsible for subunit interactions (differs between eukaryotic and bacterial enzymes), domain 3 (N-terminal of gyrA) is responsible for the breaking-rejoining function through its capacity to form protein-DNA bridges, and domain 4 (C-terminal of gyrA) is able to non-specifically bind DNA
[6]
.

Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication
[5]
. Topoisomerase IV consists of two polypeptide subunits, parE and parC, where parC is homologous to gyrA and parE is homologous to gyrB.

This superfamily represents the C-terminal domain of subunit B (gyrB and parE) of bacterial gyrase and topoisomerase IV, and the equivalent region in eukaryotic topoisomerase II composed of a single polypeptide.

References
Imported from IPR013759

1.The mechanisms of DNA topoisomerases. Roca J. Trends Biochem. Sci. 20, 156-60, (1995). View articlePMID: 7770916

2.Structure and function of type II DNA topoisomerases. Watt PM, Hickson ID. Biochem. J. 303 ( Pt 3), 681-95, (1994). View articlePMID: 7980433

3.Cellular roles of DNA topoisomerases: a molecular perspective. Wang JC. Nat. Rev. Mol. Cell Biol. 3, 430-40, (2002). View articlePMID: 12042765

4.Phylogenomics of type II DNA topoisomerases. Gadelle D, Filee J, Buhler C, Forterre P. Bioessays 25, 232-42, (2003). View articlePMID: 12596227

5.The structural basis for substrate specificity in DNA topoisomerase IV. Corbett KD, Schoeffler AJ, Thomsen ND, Berger JM. J. Mol. Biol. 351, 545-61, (2005). View articlePMID: 16023670

6.Bacterial diversity based on type II DNA topoisomerase genes. Huang WM. Annu. Rev. Genet. 30, 79-107, (1996). View articlePMID: 8982450

7.DNA topoisomerases: structure, function, and mechanism. Champoux JJ. Annu. Rev. Biochem. 70, 369-413, (2001). View articlePMID: 11395412

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