Bacterial DNA topoisomerase I DNA-binding domain
SMART accession number:SM00437
Description: Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Interpro abstract (IPR003602):

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 [(PUBMED:7770916)]. 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 [(PUBMED:12042765), (PUBMED:11395412)]. DNA topoisomerases are divided into two classes: type I enzymes (EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (EC; topoisomerases II, IV and VI) break double-strand DNA [(PUBMED:12596227)].

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.

This entry describes the DNA-binding domain (domain 3) found in type IA topoisomerases. The structures of bacterial topoisomerases I and III have been shown to consist of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA. The N-terminal Toprim domain together with domain 3 (beta-barrel) forms the active site of the enzyme, while domains 2 and 4 (both winged-helix-like) form a single-strand DNA-binding groove [(PUBMED:14604525), (PUBMED:10574789)]. All topoisomerases cleave DNA by forming a transient phosphotyrosine bond; in type IA topoisomerases, the active site tyrosine is in domain 3 [(PUBMED:14604525)].

GO process:DNA topological change (GO:0006265)
GO function:DNA topoisomerase activity (GO:0003916), DNA binding (GO:0003677)
Family alignment:
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There are 12837 TOP1Ac domains in 12837 proteins in SMART's nrdb database.

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