2O5C

Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 5.5

Summary for 2O5C

• Entry DOI: 10.2210/pdb2o5c/pdb
• Related: 1D6M 1I7D 2O19 2O54 2O59 2O5E
• Descriptor: 5'-D(*CP*GP*CP*AP*AP*CP*TP*T)-3', DNA topoisomerase 3, THYMINE, ... (5 entities in total)
• Functional Keywords: topoisomerase type ia complex with ssdna, isomerase-dna complex, isomerase/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 153273.56

Authors

Changela, A.,DiGate, R.J.,Mondragon, A. (deposition date: 2006-12-05, release date: 2007-04-03, Last modification date: 2023-08-30)

Primary citation

Changela, A.,Digate, R.J.,Mondragon, A.
Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate.
J.Mol.Biol., 368:105-118, 2007

PubMed Abstract: Escherichia coli DNA topoisomerase III belongs to the type IA family of DNA topoisomerases, which transiently cleave single-stranded DNA (ssDNA) via a 5' phosphotyrosine intermediate. We have solved crystal structures of wild-type E. coli topoisomerase III bound to an eight-base ssDNA molecule in three different pH environments. The structures reveal the enzyme in three distinct conformational states while bound to DNA. One conformation resembles the one observed previously with a DNA-bound, catalytically inactive mutant of topoisomerase III where DNA binding realigns catalytic residues to form a functional active site. Another conformation represents a novel intermediate in which DNA is bound along the ssDNA-binding groove but does not enter the active site, which remains in a catalytically inactive, closed state. A third conformation shows an intermediate state where the enzyme is still in a closed state, but the ssDNA is starting to invade the active site. For the first time, the active site region in the presence of both the catalytic tyrosine and ssDNA substrate is revealed for a type IA DNA topoisomerase, although there is no evidence of ssDNA cleavage. Comparative analysis of the various conformational states suggests a sequence of domain movements undertaken by the enzyme upon substrate binding.

PubMed: 17331537
DOI: 10.1016/j.jmb.2007.01.065

Experimental method

X-RAY DIFFRACTION (2.35 Å)