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Literature summary for 5.6.2.1 extracted from

  • Cheng, Z.; Tan, G.; Wang, W.; Su, X.; Landry, A.P.; Lu, J.; Ding, H.
    Iron and zinc binding activity of Escherichia coli topoisomerase I homolog YrdD (2014), Biometals, 27, 229-236.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
expression of YrdD protein, the homologue of the topoisomerase I C-terminal region, that contains only iron or zinc by expressing the protein in Escherichia coli cells grown in the M9 minimal media supplemented with either iron or zinc, respectively Escherichia coli

Protein Variants

Protein Variants Comment Organism
additional information preparation of YrdD protein, the homologue of the topoisomerase I C-terminal region, that contains only iron or zinc by expressing the protein in Escherichia coli cells grown in the M9 minimal media supplemented with either iron or zinc, respectively Escherichia coli

Inhibitors

Inhibitors Comment Organism Structure
Fe2+ the iron-bound enzyme fails to relax the negatively supercoiled DNA, the iron-bound YrdD has very little or no binding activity for single-stranded DNA. Iron-bound YrdD cannot protect ssDNA from the DNase I digestion Escherichia coli

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Escherichia coli
additional information topoisomerase I is able to bind both iron and zinc in the C-terminal region in vivo, unlike the zinc-bound topoisomerase I, the iron-bound enzyme fails to relax the negatively supercoiled DNA. YrdD, the homologue of the topoisomerase I C-terminal region, can also bind both iron and zinc in vivo Escherichia coli
Zn2+ required. The zinc-bound YrdD has a strong binding affinity for single-stranded DNA and protects ssDNA from the DNase I digestion in vitro. Zinc-bound YrdD can protect ssDNA from the DNase I digestion Escherichia coli

Organism

Organism UniProt Comment Textmining
Escherichia coli
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-
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Subunits

Subunits Comment Organism
More the enzyme contains an N-terminal catalytic fragment of 67 kDa and a C-terminal zinc binding region of 30 kDa Escherichia coli

Synonyms

Synonyms Comment Organism
topoisomerase I homolog
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Escherichia coli
YrdD
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Escherichia coli

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
assay at Escherichia coli

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
assay at Escherichia coli

General Information

General Information Comment Organism
evolution Escherichia coli topoisomerase I belongs to type I subfamily DNA topoisomerases. YrdD, a homolog of the C-terminal zinc binding region of Escherichia coli topoisomerase I, is highly conserved among proteobacteria and enterobacteria Escherichia coli
additional information YrdD is a homologue of the C-terminal zinc binding region of Escherichia coli topoisomerase I. The enzyme contains an N-terminal catalytic fragment and a C-terminal zinc binding region. While the N-terminal fragment is sufficient for cleaving single-stranded DNA, the C-terminal region is required for relaxing the negatively supercoiled DNA and for interacting with RNA polymerase Escherichia coli