PDBsum entry 5eix

Isomerase/DNA

PDB id: 5eix

Contents

Protein chains

702 a.a.

DNA/RNA

Ligands

LFX ×4

Metals

_MG ×8

PDB id:

5eix

Name:

Isomerase/DNA

Title:

Quinolone-stabilized cleavage complex of topoisomerase iv from klebsiella pneumoniae

Structure:

DNA topoisomerase 4 subunit b,DNA topoisomerase 4 subunit a. Chain: a, b, g, j. Synonym: topoisomerase iv subunit b,topoisomerase iv subunit a. Engineered: yes. Symmetrised e-site (pre-cut). Chain: e, c, h, k. Engineered: yes. Symmetrised e-site (pre-cut).

Source:

Klebsiella pneumoniae. Organism_taxid: 573. Strain: atcc 35657. Gene: parc, kpr_4469, sl72_02036. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

3.35Å R-factor: 0.226 R-free: 0.259

Authors:

D.A.Veselkov,I.Laponogov,X.-S.Pan,J.Selvarajah,A.Branstrom, L.M.Fisher,M.R.Sanderson

Key ref:

D.A.Veselkov et al. (2016). Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from Klebsiella pneumoniae and comparison with a related Streptococcus pneumoniae complex. Acta Crystallogr D Struct Biol, 72, 488-496. PubMed id: 27050128 DOI: 10.1107/S2059798316001212

Date:

30-Oct-15 Release date: 13-Apr-16

Protein chains

R4YE07  (R4YE07_KLEPR) -  DNA topoisomerase 4 subunit A from Klebsiella pneumoniae subsp. rhinoscleromatis SB3432

Seq: 752 a.a.

Struc: 702 a.a.*

Protein chains

R4YHS8  (R4YHS8_KLEPR) -  DNA topoisomerase 4 subunit B from Klebsiella pneumoniae subsp. rhinoscleromatis SB3432

Seq: 631 a.a.

Struc: 702 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

DNA/RNA chains

C-G-T-T-G-T-A-T 8 bases

G-A-T-C-A-T-A-C-A-A-C-G 12 bases

C-G-T-T-G-T-A-T 8 bases

G-A-T-C-A-T-A-C-A-A-C-G 12 bases

C-G-T-T-G-T-A-T 8 bases

G-A-T-C-A-T-A-C-A-A-C-G 12 bases

C-G-T-T-G-T-A-T 8 bases

G-A-T-C-A-T-A-C-A-A-C-G 12 bases

Enzyme reactions

• Enzyme class: E.C.5.6.2.2 - Dna topoisomerase (ATP-hydrolyzing).

DOI no: 10.1107/S2059798316001212

Acta Crystallogr D Struct Biol 72:488-496 (2016)

PubMed id: 27050128

Structure of a quinolone-stabilized cleavage complex of topoisomerase IV from Klebsiella pneumoniae and comparison with a related Streptococcus pneumoniae complex.

D.A.Veselkov, I.Laponogov, X.S.Pan, J.Selvarajah, G.B.Skamrova, A.Branstrom, J.Narasimhan, J.V.Prasad, L.M.Fisher, M.R.Sanderson.

ABSTRACT

Klebsiella pneumoniae is a Gram-negative bacterium that is responsible for a range of common infections, including pulmonary pneumonia, bloodstream infections and meningitis. Certain strains of Klebsiella have become highly resistant to antibiotics. Despite the vast amount of research carried out on this class of bacteria, the molecular structure of its topoisomerase IV, a type II topoisomerase essential for catalysing chromosomal segregation, had remained unknown. In this paper, the structure of its DNA-cleavage complex is reported at 3.35 Å resolution. The complex is comprised of ParC breakage-reunion and ParE TOPRIM domains of K. pneumoniae topoisomerase IV with DNA stabilized by levofloxacin, a broad-spectrum fluoroquinolone antimicrobial agent. This complex is compared with a similar complex from Streptococcus pneumoniae, which has recently been solved.