PDBsum entry 2o5e

Isomerase/DNA

PDB id: 2o5e

Contents

Protein chains

634 a.a. *

DNA/RNA

Ligands

TDR

Metals

_CL ×2

Waters ×147

* Residue conservation analysis

PDB id:

2o5e

Name:

Isomerase/DNA

Title:

Structure of e. Coli topoisomerase iii in complex with an 8-base single stranded oligonucleotide. Frozen in glucose ph 7.0

Structure:

5'-d( Cp Gp Cp Ap Ap Cp Tp T)-3'. Chain: c, d. Engineered: yes. DNA topoisomerase 3. Chain: a, b. Synonym: DNA topoisomerase iii. Engineered: yes

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: topb. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

2.50Å R-factor: 0.219 R-free: 0.260

Authors:

A.Changela,R.J.Digate,A.Mondragon

Key ref:

A.Changela et al. (2007). Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate. J Mol Biol, 368, 105-118. PubMed id: 17331537 DOI: 10.1016/j.jmb.2007.01.065

Date:

05-Dec-06 Release date: 03-Apr-07

Protein chains

P14294  (TOP3_ECOLI) -  DNA topoisomerase 3 from Escherichia coli (strain K12)

Seq: 653 a.a.

Struc: 634 a.a.*

* PDB and UniProt seqs differ at 10 residue positions (black crosses)

DNA/RNA chains

C-G-C-A-A-C-T 7 bases

C-G-C-A-A-C-T 7 bases

Enzyme reactions

• Enzyme class: E.C.5.6.2.1 - Dna topoisomerase.

DOI no: 10.1016/j.jmb.2007.01.065

J Mol Biol 368:105-118 (2007)

PubMed id: 17331537

Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate.

A.Changela, R.J.Digate, A.Mondragón.

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.

Selected figure(s)

Figure 1.
Figure 1. Overall structure of the open and closed complexes. (a) The diagram shows a schematic representation of the closed complex (Form I, pH 5.5). The four major domains of the protein are colored red, blue, purple, and green for domain I, II, III, and IV, respectively. The active site is found at the intersection of domains I and III. The ssDNA binding groove extends from domain IV to the active site. The ssDNA in the complex is shown in a ball and stick representation. (b) Schematic diagram of the open complex (Form II, pH 5.5), colored as in (a). (c) Stereo view showing the superposition of the closed (red), intermediate (blue), and open (green) complexes. The structures were aligned by superposing domain I only. The three structures correspond to Form I pH 5.5, Form II pH 8.0, and Form II, pH 5.5.

Figure 5.
Figure 5. Conformation of the ssDNA in the closed, intermediate, and closed forms. Stereo diagram of the ssDNA in the closed (red), intermediate (blue), and open (green) conformations. The diagram illustrates the differences in conformation of the ssDNA as it enters the active site. The first five nucleotides remain essentially unchanged, while nucleotides 6 and 7 change conformation to approach the active site. Nucleotide 8 is ordered only in the open conformation. Note the base of Thy 7, which is in a completely different conformation in the closed form. As the structure changes from the closed to the open forms, the phosphate of Thy 7, the scissile phosphate, approaches the active site. Nucleotides are numbered from the 5′ to the 3′ end starting at Cyt1.

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 368, 105-118) copyright 2007.

Figures were selected by an automated process.