Primary Citation PubMed: 12963818
Citations in PubMed
This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.
Data mentions are occurrences of PDB IDs in the full text articles from the
PubMedCentral Open Access Subset
of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed.
Article titles can be filtered by keywords and sorted by year.
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
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.