› 6fqm

X-ray diffraction
3.06Å resolution

3.06A COMPLEX OF S.AUREUS GYRASE with imidazopyrazinone T1 AND DNA

Released:
DOI: 10.2210/pdb6fqm/pdb
PDB entry 6fqm coloured by chain, front view.
PDB entry 6fqm coloured by chain, side view.
PDB entry 6fqm coloured by chain, top view.
Source organism: Staphylococcus aureus subsp. aureus N315
Primary publication:
A new class of antibacterials, the imidazopyrazinones, reveal structural transitions involved in DNA gyrase poisoning and mechanisms of resistance.
Germe T, Vörös J, Jeannot F, Taillier T, Stavenger RA, Bacqué E, Maxwell A, Bax BD
Nucleic Acids Res 46 4114-4128 (2018)
PMID: 29538767

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119918 (preferred)
Entry contents:
3 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (4 distinct):
DNA gyrase subunit B Chains: B, b, d
Molecule details ›
Chains: B, b, d
Length: 201 amino acids
Theoretical weight: 22.47 KDa
Source organism: Staphylococcus aureus subsp. aureus N315
Expression system: Escherichia coli
UniProt:
  • Canonical: P66937 (Residues: 410-644; Coverage: 31%)
Gene names: SA0005, gyrB
Sequence domains:
DNA gyrase subunit A Chains: A, C, a, c
Molecule details ›
Chains: A, C, a, c
Length: 490 amino acids
Theoretical weight: 55.62 KDa
Source organism: Staphylococcus aureus subsp. aureus N315
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99XG5 (Residues: 2-491; Coverage: 55%)
Gene names: SA0006, gyrA
Sequence domains: DNA gyrase/topoisomerase IV, subunit A
DNA gyrase subunit B Chain: D
Molecule details ›
Chain: D
Length: 202 amino acids
Theoretical weight: 22.61 KDa
Source organism: Staphylococcus aureus subsp. aureus N315
Expression system: Escherichia coli
UniProt:
  • Canonical: P66937 (Residues: 409-644; Coverage: 31%)
Gene names: SA0005, gyrB
Sequence domains:
DNA (5'-D(*GP*AP*GP*AP*GP*TP*AP*T*GP*GP*CP*CP*AP*TP*AP*CP*TP*CP*T)-3') Chains: E, F, e, f
Molecule details ›
Chains: E, F, e, f
Length: 20 nucleotides
Theoretical weight: 6.15 KDa

Ligands and Environments

4 bound ligands:
Ligand MN 4 x MN
Ligand SO4 2 x SO4
Ligand E32 6 x E32
Ligand GOL 1 x GOL
1 modified residue:
Ligand PTR 4 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P21
Unit cell:
a: 88.34Å b: 171.71Å c: 124.87Å
α: 90° β: 102.86° γ: 90°
R-values:
R R work R free
0.197 0.195 0.234
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Quinolones: Mechanism, Lethality and Their Contributions to Antibiotic Resistance.
Bush et al. (2020)
1 more

5 mentions without citation

DNA Topoisomerase Inhibitors: Trapping a DNA-Cleaving Machine in Motion.
Bax et al. (2019)
4 more