Homologous Superfamily

DNA topoisomerase I, DNA binding, N-terminal domain 2 (IPR013030)

Short name: DNA_topo_DNA_db_N_dom2

Description

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 [PMID: 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 [PMID: 12042765, PMID: 11395412]. DNA topoisomerases are divided into two classes: type I enzymes (EC:5.99.1.2; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (EC:5.99.1.3; topoisomerases II, IV and VI) break double-strand DNA [PMID: 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 (Topo IA; bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (Topo 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 function is vital for the processes of replication, transcription, and recombination. Unlike Topo IA enzymes, Topo IB enzymes do not require a single-stranded region of DNA or metal ions for their function. The type IB family of DNA topoisomerases includes eukaryotic nuclear topoisomerase I, topoisomerases of poxviruses, and bacterial versions of Topo IB [PMID: 17293019]. They belong to the superfamily of DNA breaking-rejoining enzymes, which share the same fold in their C-terminal catalytic domain and the overall reaction mechanism with tyrosine recombinases [PMID: 21087076,PMID: 9488644]. The C-terminal catalytic domain in topoisomerases is linked to a divergent N-terminal domain that shows no sequence or structure similarity to the N-terminal domains of tyrosine recombinases [PMID: 20644584,PMID: 17722649].

This entry represents a structural motif, consisting of a complex alpha/beta topology that forms the N-terminal DNA-binding domain of certain eukaryotic topoisomerase I (type IB) enzymes. To cleave the DNA backbone, these enzymes must make a transient phosphotyrosine bond. The N-terminal domain of human topoisomerase I is thought to coordinate the restriction of free strand rotation during the topoisomerisation step of catalysis. A conserved tryptophan residue may be important for the DNA-interaction ability of the N-terminal domain [PMID: 14741206]. Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes [PMID: 9488644].

GO terms

Biological Process

GO:0006265 DNA topological change

Molecular Function

GO:0003677 DNA binding
GO:0003917 DNA topoisomerase type I activity

Cellular Component

GO:0005694 chromosome

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
GENE3D