PDBsum entry: 1zvu

Isomerase

PDB id: 1zvu

Contents

Protein chain

685 a.a. *

Waters ×35

* Residue conservation analysis

PDB id:

1zvu

Name:

Isomerase

Title:

Structure of the full-length e. Coli parc subunit

Structure:

Topoisomerase iv subunit a. Chain: a. Fragment: parc27 (residues 27-742). Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: parc. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

3.00Å R-factor: 0.243 R-free: 0.296

Authors:

K.D.Corbett,A.J.Schoeffler,N.D.Thomsen,J.M.Berger

Key ref:

K.D.Corbett et al. (2005). The structural basis for substrate specificity in DNA topoisomerase IV. J Mol Biol, 351, 545-561. PubMed id: 16023670 DOI: 10.1016/j.jmb.2005.06.029

Date:

02-Jun-05 Release date: 05-Jul-05

Protein chain

P0AFI2  (PARC_ECOLI) -  DNA topoisomerase 4 subunit A

Seq: 752 a.a.

Struc: 685 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (3 terms)
• Biological process: DNA metabolic process (3 terms)
• Biochemical function: isomerase activity (5 terms)

DOI no: 10.1016/j.jmb.2005.06.029

J Mol Biol 351:545-561 (2005)

PubMed id: 16023670

The structural basis for substrate specificity in DNA topoisomerase IV.

K.D.Corbett, A.J.Schoeffler, N.D.Thomsen, J.M.Berger.

ABSTRACT

Most bacteria possess two type IIA topoisomerases, DNA gyrase and topo IV, that together help manage chromosome integrity and topology. Gyrase primarily introduces negative supercoils into DNA, an activity mediated by the C-terminal domain of its DNA binding subunit (GyrA). Although closely related to gyrase, topo IV preferentially decatenates DNA and relaxes positive supercoils. Here we report the structure of the full-length Escherichia coli ParC dimer at 3.0 A resolution. The N-terminal DNA binding region of ParC is highly similar to that of GyrA, but the ParC dimer adopts a markedly different conformation. The C-terminal domain (CTD) of ParC is revealed to be a degenerate form of the homologous GyrA CTD, and is anchored to the top of the N-terminal domains in a configuration different from that thought to occur in gyrase. Biochemical assays show that the ParC CTD controls the substrate specificity of topo IV, likely by capturing DNA segments of certain crossover geometries. This work delineates strong mechanistic parallels between topo IV and gyrase, while explaining how structural differences between the two enzyme families have led to distinct activity profiles. These findings in turn explain how the structures and functions of bacterial type IIA topoisomerases have evolved to meet specific needs of different bacterial families for the control of chromosome superstructure.

Selected figure(s)

Figure 2.
Figure 2. Structure of the full-length ParC subunit. (a) Overall structure of the ParC27 dimer. The CAP domain is colored purple, the tower blue, the dimerization domain and connecting a-helices red, the CTD green, and the active site Arg119 and Tyr120 shown as yellow sticks. The conformation of the dimer is splayed open compared to the structure of the E. coli GyrA NTD or S. cerevisiaetopo II (Figure 3).41^, 42^ and 43 (b) Close-up of the region outlined by the broken box in (a), highlighting the ordered NTD-CTD linker (residues 481-499). Electron density shown is a portion of a simulated-annealing composite all-omit F[o]-F[c] map, contoured at 2.0s. (c) View equivalent to (b), showing the hydrophobic "ball joint" formed by two methionine residues on the linker (Met489 and Met494) docking into a hydrophobic pocket on the tower domain (the yellow surface contains residues Leu279, Met281, Val306, Met308, and Val311).

Figure 3.
Figure 3. Comparison of GyrA and ParC NTD conformations. (a) The N-terminal regions of GyrA41 (gray) and ParC (blue) are presented side-by-side. Shown in red are a pair of a-helices that connect the dimerization domain to the CAP and tower domains. Top-down views show that a twisting motion accompanies the separation of the CAP domains (arrows). (b) Stereo view of an overlay of one dimerization domain from GyrA (gray) and ParC (red), showing the flexion of the connector helices that leads to the global conformational differences observed between the two structures. Not shown in this panel is an insertion in the dimerization domain (residues 413-451) specific to GyrA. (c) Top-down view of the active site of ParC (purple) overlaid with that of GyrA (gray and cyan, dimer mate in gray surface). The reconfigured loop in the CAP domain (residues 102-124 of ParC) is shown with active-site arginine and tyrosine residues (labeled) in stick representation.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 351, 545-561) copyright 2005.

Figures were selected by an automated process.