› 6waa

X-ray diffraction
3.2Å resolution

K. pneumoniae Topoisomerase IV (ParE-ParC) in complex with DNA and compound 34 (7-[(1S,5R)-1-amino-3-azabicyclo[3.1.0]hexan-3-yl]-4-(aminomethyl)-1-cyclopropyl-3,6-difluoro-8-methylquinolin-2(1H)-one)

Released:
DOI: 10.2210/pdb6waa/pdb
PDB entry 6waa coloured by chain, front view.
PDB entry 6waa coloured by chain, side view.
PDB entry 6waa coloured by chain, top view.
Source organism: Klebsiella pneumoniae 342
Primary publication:
Topoisomerase Inhibitors Addressing Fluoroquinolone Resistance in Gram-Negative Bacteria.
Skepper CK, Armstrong D, Balibar CJ, Bauer D, Bellamacina C, Benton BM, Bussiere D, De Pascale G, De Vicente J, Dean CR, Dhumale B, Fisher LM, Fuller J, Fulsunder M, Holder LM, Hu C, Kantariya B, Lapointe G, Leeds JA, Li X, Lu P, Lvov A, Ma S, Madhavan S, Malekar S, McKenney D, Mergo W, Metzger L, Moser HE, Mutnick D, Noeske J, Osborne C, Patel A, Patel D, Patel T, Prajapati K, Prosen KR, Reck F, Richie DL, Rico A, Sanderson MR, Satasia S, Sawyer WS, Selvarajah J, Shah N, Shanghavi K, Shu W, Thompson KV, Traebert M, Vala A, Vala L, Veselkov DA, Vo J, Wang M, Widya M, Williams SL, Xu Y, Yue Q, Zang R, Zhou B, Rivkin A
J Med Chem 63 7773-7816 (2020)
PMID: 32634310

Function and Biology Details

Reaction catalysed: 
ATP-dependent breakage, passage and rejoining of double-stranded DNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110264 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA topoisomerase 4 subunit A Chains: B, D, F, H
Molecule details ›
Chains: B, D, F, H
Length: 743 amino acids
Theoretical weight: 84.28 KDa
Source organism: Klebsiella pneumoniae 342
Expression system: Escherichia coli
UniProt:
  • Canonical: B5XU60 (Residues: 1-490; Coverage: 65%)
Gene names: KPK_0685, parC
Sequence domains: DNA gyrase/topoisomerase IV, subunit A
DNA (5'-D(*TP*TP*AP*CP*GP*TP*TP*GP*TP*AP*T)-3') Chains: I, L, M, P
Molecule details ›
Chains: I, L, M, P
Length: 11 nucleotides
Theoretical weight: 3.35 KDa
Source organism: Klebsiella pneumoniae 342
Expression system: Not provided
DNA (5'-D(*GP*AP*TP*CP*AP*TP*AP*CP*AP*AP*CP*GP*TP*AP*A)-3') Chains: J, K, N, O
Molecule details ›
Chains: J, K, N, O
Length: 15 nucleotides
Theoretical weight: 4.59 KDa
Source organism: Klebsiella pneumoniae 342
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand MPD 6 x MPD
Ligand MG 11 x MG
Ligand CL 2 x CL
Ligand TNJ 4 x TNJ
1 modified residue:
Ligand PTR 4 x PTR

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P21
Unit cell:
a: 94.59Å b: 157.481Å c: 144.06Å
α: 90° β: 94.93° γ: 90°
R-values:
R R work R free
0.275 0.274 0.301
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

What makes a type IIA topoisomerase a gyrase or a Topo IV?
Hirsch et al. (2021)
3 other articles