TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain
SMART ACC:	SM000437
Description:	Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
InterPro ACC:	IPR003602
InterPro abstract:	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 … expand 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:5.6.2.2 ; topoisomerases I, III and V) break single-strand DNA, and type II enzymes ( EC:5.6.2.2 ; 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 (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 [ PUBMED: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 [ PUBMED:21087076 PUBMED: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 [ PUBMED:20644584 PUBMED:17722649 ]. 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 (β-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 ]. collapse
GO process:	DNA topological change (GO:0006265)
GO function:	DNA binding (GO:0003677), DNA topoisomerase activity (GO:0003916)
Family alignment:	View the Family alignment or the Alignment consensus sequence
There are 39 927 TOP1Ac domains in 39 925 proteins in SMART's NRDB database.

Taxonomic distribution of proteins containing TOP1Ac domains

The tree below includes only several representative species and genera. The complete taxonomic breakdown of all proteins containing TOP1Ac domains can be accessed here. Click the counts or percentage values to display the corresponding proteins.

Relevant references for this domain

Primary literature for the TOP1Ac domain is listed below. Automatically-derived, secondary literature is also available.

KEGG pathways involving proteins which contain this domain

This information is based on the mapping of SMART genomic protein database to KEGG orthologous groups. Percentages are related to the number of proteins containing a TOP1Ac domain which could be assigned to a KEGG orthologous group, and not all proteins containing TOP1Ac domains. Please note that proteins can be included in multiple pathways, ie. the numbers below will not add to 100%.

KEGG pathways

Some of these pathways are included in the interactive Pathways Explorer overview maps. Select an overview map and click the button below to highlight them in iPath.

KEGG orthologous groups

Some of these KOs are included in the interactive Pathways Explorer overview maps. Select an overview map and click the button below to highlight them in iPath.

3D structures in PDB containing this domain

Links to other resources describing this domain

Pfam	Topoisom_bac
InterPro	IPR003602
PROSITE	TOPOISOMERASE_I_PROK