Primary Citation PubMed: 12963818
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Analysis of the eukaryotic topoisomerase II DNA gate: a single-molecule FRET and structural perspective.
(2009) Nucleic Acids Res 37
PubMed: 19155278 | PubMedCentral: PMC2647300 | DOI: 10.1093/nar/gkn1059
Structures of Saccharomyces cerevisiae topo II (PDB 1PVG and 1BGW) were computationally docked together to illustrate a possible representation of the enzyme.
Publication Year: 2009
Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity.
(2012) Nat Struct Mol Biol 19
PubMed: 23022727 | PubMedCentral: PMC3492516 | DOI: 10.1038/nsmb.2388
The first model corresponded to a single, DNA-free promoter from the cleavage complex of the S. cerevisiae topo II DNA binding and cleavage core (residues 421–1177 of PDB ID code 3L4J) 27 , an... the second to one protomer from the S. cerevisiae topo II ATPase domain dimer (residues 7-406 of PDB ID code 1PVG) 17 .
Publication Year: 2012
PubMed ID is not available.
Published in 2015
Table 3 Summary of selected homologous PDB entries described in this study Protein Source PDB code Resolution () Aligned residues † R.m.s. deviation † () Identity † (%) Site 1 ... ccupancy Reference GyrB43 E. coli 4pu9 2.40 353 0.69 99.7 Water Stanger et al. (2014 ▶ ) GyrB43 E. coli 1ei1 2.30 383 0.52 99.5 Water Brino et al. (2000 ▶ ) ParE E. coli 1s16 2.10 354 1.37 36.2 Mg 2+ ‡ Bellon et al. (2004 ▶ ) Topo II S. cerevisiae 1pvg 1.80 302 2.04 24.8 N of Lys Classen et al. (2003 ▶ ) Topo II H. sapiens 1zxn 2.51 281 1.97 22.1 N of Lys Wei et al. (2005 ▶ ) MutL E. coli 1nhi 2.00 270 3.18 15.9 K + Hu et al. (2003 ▶ ) Topo VIB S. shibatae 1mx0 2.30 235 2.28 15.7 N of Lys Corbett Berger (2003 ▶ ) BCK R. norvegicus 1gkz 2.20 107 1.95 21.5 K + Machius et al. (2001 ▶ ) † Values determined using the Secondary Structure Matching ( SSM ) algorithm within Coot (Emsley Cowtan, 2004 ▶ ) to superpose structures on the K-only GyrB43 model.
Intriguingly, we noted that in the eukaryotic topoisomerase II (topo II) structures from yeast and human (PDB entries 1pvg and 1zxn , respectively; Classen et al. , 2003 ▶ ; Wei et al. , 2005 ▶ ) the residue corresponding to Ser121 of E. coli GyrB was substituted by a Lys.
( d ) Equivalent site in yeast topoisomerase II (PDB entry 1pvg ) showing how the N ζ atom of Lys147 effectively substitutes for the K + ion seen in the GyrB43 K-only structure.
Publication Year: 2015
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