4I3H

A three-gate structure of topoisomerase IV from Streptococcus pneumoniae

Summary for 4I3H

• Entry DOI: 10.2210/pdb4i3h/pdb
• Related: 1EI1 2NOV 3FOE 3FOF 3K9F 3KSA 3KSB 3LTN 3RAD 3RAE 3RAF 4GFH
• Descriptor: DNA (5'-D(*CP*AP*AP*AP*GP*GP*CP*GP*GP*TP*AP*AP*TP*AP*CP*GP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*AP*AP*TP*CP*AP*GP*G)-3'), DNA (5'-D(*CP*CP*TP*GP*AP*TP*TP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*CP*GP*TP*AP*TP*TP*AP*CP*CP*GP*CP*CP*TP*TP*TP*G)-3'), Topoisomerase IV subunit B, DNA topoisomerase 4 subunit A chimera, ... (5 entities in total)
• Functional Keywords: dna unwinding, supercoiling, isomerase-dna complex, isomerase/dna
• Biological source: Streptococcus pneumoniae; More
• Cellular location: Cell membrane ; Peripheral membrane protein : D6ZLV0
• Total number of polymer chains: 6
• Total formula weight: 298555.59

Authors

Laponogov, I.,Veselkov, D.A.,Pan, X.-S.,Crevel, I.,Fisher, L.M.,Sanderson, M.R. (deposition date: 2012-11-26, release date: 2013-08-28, Last modification date: 2023-09-20)

Primary citation

Laponogov, I.,Veselkov, D.A.,Crevel, I.M.,Pan, X.S.,Fisher, L.M.,Sanderson, M.R.
Structure of an 'open' clamp type II topoisomerase-DNA complex provides a mechanism for DNA capture and transport.
Nucleic Acids Res., 41:9911-9923, 2013

PubMed Abstract: Type II topoisomerases regulate DNA supercoiling and chromosome segregation. They act as ATP-operated clamps that capture a DNA duplex and pass it through a transient DNA break in a second DNA segment via the sequential opening and closure of ATPase-, G-DNA- and C-gates. Here, we present the first 'open clamp' structures of a 3-gate topoisomerase II-DNA complex, the seminal complex engaged in DNA recognition and capture. A high-resolution structure was solved for a (full-length ParE-ParC55)2 dimer of Streptococcus pneumoniae topoisomerase IV bound to two DNA molecules: a closed DNA gate in a B-A-B form double-helical conformation and a second B-form duplex associated with closed C-gate helices at a novel site neighbouring the catalytically important β-pinwheel DNA-binding domain. The protein N gate is present in an 'arms-wide-open' state with the undimerized N-terminal ParE ATPase domains connected to TOPRIM domains via a flexible joint and folded back allowing ready access both for gate and transported DNA segments and cleavage-stabilizing antibacterial drugs. The structure shows the molecular conformations of all three gates at 3.7 Å, the highest resolution achieved for the full complex to date, and illuminates the mechanism of DNA capture and transport by a type II topoisomerase.

PubMed: 23965305
DOI: 10.1093/nar/gkt749

Experimental method

X-RAY DIFFRACTION (3.7 Å)