G3DSA:2.120.10.90

DNA gyrase/topoisomerase IV, subunit A, C-terminal

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

Description
Imported from IPR035516

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
[9]
. 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
[6, 1]
. 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
[5]
.

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
[4]
.

This entry represents the β-pinwheel continuous domain found at the C-terminal end of subunit A of topoisomerase IV (ParC) and subunit A of DNA gyrase (GyrA)
[3]
. DNA gyrase is the topoisomerase II found primarily in bacteria and archaea that consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. This is distinct from the topoisomerase II found in most eukaryotes, which consists of a single polypeptide, with the N- and C-terminal regions corresponding to gyrB and gyrA, respectively, and which is not represented in this entry.

The ability of DNA gyrase to introduce negative supercoils into DNA is mediated in part by the C-terminal domain of subunit A, which forms a β-pinwheel fold that is similar to a β-propeller but with a different blade topology, and which forms a superhelical spiral domain
[3, 7]
. This β-pinwheel is capable of bending DNA by over 180 degrees over a 40 bp region, possibly by wrapping the DNA around the GyrA C-terminal β-pinwheel domain.

In topoisomerase IV, although the C-terminal domain forms a similar superhelical spiral to that of DNA gyrase A, it assembles as a broken form of a β-pinwheel as distinct from that of gyrA, due to the absence of a DNA gyrase-specific GyrA box motif
[8]
. This difference may account for parC being less efficient than gyrA in mediating DNA-bending, leading to their divergence in terms of activity, where topoisomerase IV acts to relax positive supercoils, and DNA gyrase acts to introduce negative supercoils
[2]
.

References
Imported from IPR035516

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

2.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

3.The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold. Corbett KD, Shultzaberger RK, Berger JM. Proc. Natl. Acad. Sci. U.S.A. 101, 7293-8, (2004). View articlePMID: 15123801

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

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

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

7.A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. Ruthenburg AJ, Graybosch DM, Huetsch JC, Verdine GL. J. Biol. Chem. 280, 26177-84, (2005). View articlePMID: 15897198

8.Structure of the topoisomerase IV C-terminal domain: a broken beta-propeller implies a role as geometry facilitator in catalysis. Hsieh TJ, Farh L, Huang WM, Chan NL. J. Biol. Chem. 279, 55587-93, (2004). View articlePMID: 15466871

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

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