PDBsum entry: 2o19

Isomerase/DNA

PDB-id: 2o19

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Description

Header details

Header records

References

PROCHECK

Protein chains

630 a.a. *

DNA/RNA

Ligands

ACY

Metal ions

_CL ×2

Waters ×219

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2o19

Name:

Isomerase/DNA

Title:

Structure of e. Coli topoisomersae iii in complex with an 8- base single stranded oligonucleotide. Frozen in glycerol at ph 5.5

Structure:

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

UniProt:

Chains A, B: P14294 (TOP3_ECOLI)

Seq:

Struc:

Seq:

Struc:

Seq:

653 a.a.

Struc:

630 a.a.*

Key:

PfamA domain

Secondary structure

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

Enzyme class:

E.C.5.99.1.2   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.

Resolution:

2.45Å

R-factor:

0.214

R-free:

0.246

Authors:

A.Changela,R.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:

28-Nov-06

Release date:

03-Apr-07

Related entries:

1i7d
noncovalent complex of e.Coli DNA topoisomerase iii with an
8-base single-stranded DNA oligonucleotide
1d6m
crystal structure of e. Coli DNA topoisomerase iii
2o54
structural studies of e. Coli topoisomerase iii-DNA
complexes reveal a novel type ia topoisoemrase-DNA
conformational intermediate
2o59
... plus others (see Header records)

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Surface

Key reference

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.