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Isomerase PDB id
2nov
Jmol
Contents
Protein chains
440 a.a. *
Waters ×24
* Residue conservation analysis
PDB id:
2nov
Name: Isomerase
Title: Breakage-reunion domain of s.Pneumoniae topo iv: crystal structure of a gram-positive quinolone target
Structure: DNA topoisomerase 4 subunit a. Chain: a, b, c, d. Fragment: 55-kda n-terminal fragment. Synonym: topoisomerase iv subunit a. Engineered: yes
Source: Streptococcus pneumoniae. Organism_taxid: 1313. Strain: 7785. Gene: parc. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.67Å     R-factor:   0.224     R-free:   0.276
Authors: I.Laponogov,D.A.Veselkov,M.K.Sohi,X.S.Pan,A.Achari,C.Yang, J.D.Ferrara,L.M.Fisher,M.R.Sanderson
Key ref: I.Laponogov et al. (2007). Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target. Plos One, 2, e301. PubMed id: 17375187 DOI: 10.1371/journal.pone.0000301
Date:
26-Oct-06     Release date:   14-Nov-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P72525  (PARC_STRPN) -  DNA topoisomerase 4 subunit A
Seq:
Struc: 		 
Seq:
Struc: 		823 a.a.
440 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     chromosome   1 term 
  Biological process     DNA metabolic process   3 terms 
  Biochemical function     DNA binding     4 terms  

 

 
DOI no: 10.1371/journal.pone.0000301 Plos One 2:e301 (2007)
PubMed id: 17375187  
 
 
Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target.
I.Laponogov, D.A.Veselkov, M.K.Sohi, X.S.Pan, A.Achari, C.Yang, J.D.Ferrara, L.M.Fisher, M.R.Sanderson.
 
  ABSTRACT  
 
The 2.7 A crystal structure of the 55-kDa N-terminal breakage-reunion domain of topoisomerase (topo) IV subunit A (ParC) from Streptococcus pneumoniae, the first for the quinolone targets from a gram-positive bacterium, has been solved and reveals a 'closed' dimer similar in fold to Escherichia coli DNA gyrase subunit A (GyrA), but distinct from the 'open' gate structure of Escherichia coli ParC. Unlike GyrA whose DNA binding groove is largely positively charged, the DNA binding site of ParC exhibits a distinct pattern of alternating positively and negatively charged regions coincident with the predicted positions of the grooves and phosphate backbone of DNA. Based on the ParC structure, a new induced-fit model for sequence-specific recognition of the gate (G) segment by ParC has been proposed. These features may account for the unique DNA recognition and quinolone targeting properties of pneumococcal type II topoisomerases compared to their gram-negative counterparts.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20675723 A.J.Schoeffler, A.P.May, and J.M.Berger (2010).
A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function.
  Nucleic Acids Res, 38, 7830-7844.
PDB code: 3nuh
20165898 C.Sissi, and M.Palumbo (2010).
In front of and behind the replication fork: bacterial type IIA topoisomerases.
  Cell Mol Life Sci, 67, 2001-2024.  
20596531 I.Laponogov, X.S.Pan, D.A.Veselkov, K.E.McAuley, L.M.Fisher, and M.R.Sanderson (2010).
Structural basis of gate-DNA breakage and resealing by type II topoisomerases.
  PLoS One, 5, e11338.
PDB codes: 3k9f 3ksa 3ksb 3ltn
20805881 J.Piton, S.Petrella, M.Delarue, G.André-Leroux, V.Jarlier, A.Aubry, and C.Mayer (2010).
Structural insights into the quinolone resistance mechanism of Mycobacterium tuberculosis DNA gyrase.
  PLoS One, 5, e12245.
PDB codes: 3ifz 3ig0 3m4i
19666507 A.Gubaev, M.Hilbert, and D.Klostermeier (2009).
The DNA-gate of Bacillus subtilis gyrase is predominantly in the closed conformation during the DNA supercoiling reaction.
  Proc Natl Acad Sci U S A, 106, 13278-13283.  
19448616 I.Laponogov, M.K.Sohi, D.A.Veselkov, X.S.Pan, R.Sawhney, A.W.Thompson, K.E.McAuley, L.M.Fisher, and M.R.Sanderson (2009).
Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases.
  Nat Struct Mol Biol, 16, 667-669.
PDB codes: 3foe 3fof
19279051 S.Malhotra-Kumar, L.Van Heirstraeten, C.Lammens, S.Chapelle, and H.Goossens (2009).
Emergence of high-level fluoroquinolone resistance in emm6 Streptococcus pyogenes and in vitro resistance selection with ciprofloxacin, levofloxacin and moxifloxacin.
  J Antimicrob Chemother, 63, 886-894.  
19564360 X.S.Pan, K.A.Gould, and L.M.Fisher (2009).
Probing the differential interactions of quinazolinedione PD 0305970 and quinolones with gyrase and topoisomerase IV.
  Antimicrob Agents Chemother, 53, 3822-3831.  
18755053 A.J.Schoeffler, and J.M.Berger (2008).
DNA topoisomerases: harnessing and constraining energy to govern chromosome topology.
  Q Rev Biophys, 41, 41.  
18787651 M.K.Sohi, D.A.Veselkov, I.Laponogov, X.S.Pan, L.M.Fisher, and M.R.Sanderson (2008).
The difficult case of crystallization and structure solution for the ParC55 breakage-reunion domain of topoisomerase IV from Streptococcus pneumoniae.
  PLoS ONE, 3, e3201.  
18625781 M.T.Black, T.Stachyra, D.Platel, A.M.Girard, M.Claudon, J.M.Bruneau, and C.Miossec (2008).
Mechanism of action of the antibiotic NXL101, a novel nonfluoroquinolone inhibitor of bacterial type II topoisomerases.
  Antimicrob Agents Chemother, 52, 3339-3349.  
18723572 X.S.Pan, M.Dias, M.Palumbo, and L.M.Fisher (2008).
Clerocidin selectively modifies the gyrase-DNA gate to induce irreversible and reversible DNA damage.
  Nucleic Acids Res, 36, 5516-5529.  
17766248 S.N.Richter, G.Giaretta, V.Comuzzi, E.Leo, L.A.Mitchenall, L.M.Fisher, A.Maxwell, and M.Palumbo (2007).
Hot-spot consensus of fluoroquinolone-mediated DNA cleavage by Gram-negative and Gram-positive type II DNA topoisomerases.
  Nucleic Acids Res, 35, 6075-6085.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.