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Literature summary for 5.6.2.1 extracted from

  • Zhang, Z.; Cheng, B.; Tse-Dinh, Y.C.
    Crystal structure of a covalent intermediate in DNA cleavage and rejoining by Escherichia coli DNA topoisomerase I (2011), Proc. Natl. Acad. Sci. USA, 108, 6939-6944.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 5.6.2.1

Crystallization (Commentary)

Crystallization (Comment) Organism
D111N mutant topoisomerase I catalytic domain, residues 2-695, in covalent complex with a cleaved single-stranded oligonucleotide substrate, X-ray diffraction structure determination and analysis at 2.3 A resolution Escherichia coli

Protein Variants

Protein Variants Comment Organism
D111N site-directed mutagenesis, the mutant is trapped in complex with DNA, accumulation of the covalent complex of bacterial topoisomerase I is lethal. A full-length enzyme with this D111N mutation could not be expressed, but the N-terminal 67-kDa transesterification domain. Structure comparison of wild-type and D111N mutant enzymes, overview Escherichia coli

Localization

Localization Comment Organism GeneOntology No. Textmining
nucleus
-
 Escherichia coli 5634
-

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Escherichia coli

Organism

Organism UniProt Comment Textmining
Escherichia coli
-
-
-

Reaction

Reaction Comment Organism Reaction ID
ATP-independent breakage of single-stranded DNA, followed by passage and rejoining catalytic mechanism of DNA cleavage/religation and molecular basis for selectivity of a cytosine base at the -4 position. E9 acts as a general base in DNA cleavage, assisted by charge relay through D111 and H365 Escherichia coli
a

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information the enzyme structure with bound DNA shows distinct conformational changes from the structure of the enzyme without bound DNA, overview. The portion of cleaved DNA 5' to the site of cleavage is anchored tightly with extensive noncovalent protein-DNA interactions. The portion of the oligonucleotide 5' to the cleavage site binds in a deep groove formed at the interface of domains I and III as well as within domain IV, in a similar orientation. Residues R195 and R321 are required for DNA cleavage Escherichia coli ?
-
 ?

Subunits

Subunits Comment Organism
More the enzyme structure with bound DNA shows distinct conformational changes from the structure of the enzyme without bound DNA, overview. The portion of cleaved DNA 5' to the site of cleavage is anchored tightly with extensive noncovalent protein-DNA interactions. The portion of the oligonucleotide 5' to the cleavage site binds in a deep groove formed at the interface of domains I and III as well as within domain IV, in a similar orientation. Structure comparison of wild-type and D111N mutant enzymes, overview Escherichia coli

Synonyms

Synonyms Comment Organism
Topoisomerase I
-
 Escherichia coli

General Information

General Information Comment Organism
additional information many antibacterial and anticancer drugs initiate cell killing by trapping the covalent complexes formed by topoisomerases Escherichia coli