SMART: TOP1Bc domain annotation

TOP1Bc Bacterial DNA topoisomeraes I ATP-binding domain

SMART accession number:	SM00436
Description:	Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit
Interpro abstract (IPR003601):	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 5.99.1.2; 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 [(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 domain 2 found in type IA topoisomerases, which may be an extension of the Toprim domain. 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 forms the active site of the enzyme, while domains 2 and 4 form a single-strand DNA-binding groove [(PUBMED:14604525), (PUBMED:10574789)]. The Toprim domain (IPR006171) forms a compact Rossmann fold that coordinates the Mg+2 ion [(PUBMED:9722641)]. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].
GO process:	DNA topological change (GO:0006265)
GO component:	chromosome (GO:0005694)
GO function:	DNA topoisomerase activity (GO:0003916), DNA binding (GO:0003677)
Family alignment:	View or

There are 3690 TOP1Bc domains in 3690 proteins in SMART's nrdb database.

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Evolution (species in which this domain is found)
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This tree shows only several representative species. The complete taxonomic breakdown of all proteins with TOP1Bc domain is also avaliable.

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Go to specific node: Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Takifugu rubripes
Literature (relevant references for this domain)
Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.
- Sharma A, Mondragon A
- DNA topoisomerases.
- Curr Opin Struct Biol. 1995; 5: 39-47
- Display abstract
- In the past year, the atomic structures of three fragments of type I DNA topoisomerases were elucidated. Together with the atomic structure of a fragment of bacterial gyrase, this wealth of structural information is helping to further our understanding of the mechanism of action of topoisomerases.
- Lima CD, Wang JC, Mondragon A
- Three-dimensional structure of the 67K N-terminal fragment of E. coli DNA topoisomerase I.
- Nature. 1994; 367: 138-46
- Display abstract
- The three-dimensional structure of the 67K amino-terminal fragment of Escherichia coli DNA topoisomerase I has been determined to 2.2 A resolution. The polypeptide folds in an unusual way to give four distinct domains enclosing a hole large enough to accommodate a double-stranded DNA. The active-site tyrosyl residue, which is involved in the transient breakage of a DNA strand and the formation of a covalent enzyme-DNA intermediate, is present at the interface of two domains. The structure suggests a plausible mechanism by which E. coli DNA topoisomerase I and other members of the same DNA topoisomerase subfamily could catalyse the passage of one DNA strand through a transient break in another strand.
Structure (3D structures containing this domain)

3D Structures of TOP1Bc domains in PDB

PDB code	Main view	Title
1cy0		Complex of e.coli dna topoisomerase i with 3'-5'-adenosine diphosphate
1cy1		Complex of e.coli dna topoisomerase i with 5'ptptpt
1cy2		Complex of e.coli dna topoisomerase i with tptptp3'
1cy4		Complex of e.coli dna topoisomerase i with 5'ptptptp3'
1cy6		Complex of e.coli dna topoisomerase i with 3' thymidine monophosphate
1cy7		Complex of e.coli dna topoisomerase i with 5'-thymidine monophosphate
1cy8		Complex of e.coli dna topoisomerase i with 5'-thymidine monophosphate and 3'-thymidine monophosphate
1d6m		Crystal structure of e. coli dna topoisomerase iii
1ecl		Amino terminal 67kda domain of escherichia coli dna topoisomerase i (residues 2-590 of mature protein) cloning artifact adds two residues to the amino-terminus which were not observed in the experimental electron density (gly-2, ser-1).
1gku		Reverse gyrase from archaeoglobus fulgidus
1gl9		Archaeoglobus fulgidus reverse gyrase complexed with adpnp
1i7d		Noncovalent complex of e.coli dna topoisomerase iii with an 8-base single-stranded dna oligonucleotide
1mw8		Crystal structure of a complex between h365r mutant of 67 kda n-terminal fragment of e. coli dna topoisomerase i and 5'-acttcgggatg-3'
1mw9		Crystal structure of h365r mutant of 67 kda n-terminal fragment of e. coli dna topoisomerase i
2gai		Structure of full length topoisomerase i from thermotoga maritima in triclinic crystal form
2gaj		Structure of full length topoisomerase i from thermotoga maritima in monoclinic crystal form
2o19		Structure of e. coli topoisomersae iii in complex with an 8- base single stranded oligonucleotide. frozen in glycerol at ph 5.5
2o54		Structure of e. coli topoisomerase iii in complex with an 8- base single stranded oligonucleotide. frozen in glycerol at ph 7.0
2o59		Structure of e. coli topoisomerase iii in complex with an 8- base single stranded oligonucleotide. frozen in glycerol ph 8.0
2o5c		Structure of e. coli topoisomerase iii in complex with an 8- base single stranded oligonucleotide. frozen in glucose ph 5.5
2o5e		Structure of e. coli topoisomerase iii in complex with an 8- base single stranded oligonucleotide. frozen in glucose ph 7.0

Links (links to other resources describing this domain)
PFAM Topoisom_bac
INTERPRO IPR003601
PROSITE TOPOISOMERASE_I_PROK

PFAM	Topoisom_bac
INTERPRO	IPR003601
PROSITE	TOPOISOMERASE_I_PROK