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PDBsum entry 1ab4
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Topoisomerase PDB id
1ab4

 

 

 

 

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Contents
Protein chain
477 a.a. *
Waters ×15
* Residue conservation analysis
PDB id:
1ab4
Name: Topoisomerase
Title: 59kda fragment of gyrase a from e. Coli
Structure: Gyrase a. Chain: a. Fragment: 59kda fragment. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
2.80Å     R-factor:   0.226     R-free:   0.310
Authors: J.H.M.Cabral,A.Maxwell,R.C.Liddington
Key ref:
J.H.Morais Cabral et al. (1997). Crystal structure of the breakage-reunion domain of DNA gyrase. Nature, 388, 903-906. PubMed id: 9278055 DOI: 10.1038/42294
Date:
03-Feb-97     Release date:   14-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0AES4  (GYRA_ECOLI) -  DNA gyrase subunit A from Escherichia coli (strain K12)
Seq:
Struc: 		 
Seq:
Struc: 		875 a.a.
477 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.6.2.2  - Dna topoisomerase (ATP-hydrolyzing).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1038/42294 Nature 388:903-906 (1997)
PubMed id: 9278055  
 
 
Crystal structure of the breakage-reunion domain of DNA gyrase.
J.H.Morais Cabral, A.P.Jackson, C.V.Smith, N.Shikotra, A.Maxwell, R.C.Liddington.
 
  ABSTRACT  
 
DNA gyrase is a type II DNA topoisomerase from bacteria that introduces supercoils into DNA. It catalyses the breakage of a DNA duplex (the G segment), the passage of another segment (the T segment) through the break, and then the reunification of the break. This activity involves the opening and dosing of a series of molecular 'gates' which is coupled to ATP hydrolysis. Here we present the crystal structure of the 'breakage-reunion' domain of the gyrase at 2.8 A resolution. Comparison of the structure of this 59K (relative molecular mass, 59,000) domain with that of a 92K fragment of yeast topoisomerase II reveals a very different quaternary organization, and we propose that the two structures represent two principal conformations that participate in the enzymatic pathway. The gyrase structure reveals a new dimer contact with a grooved concave surface for binding the G segment and a cluster of conserved charged residues surrounding the active-site tyrosines. It also shows how breakage of the G segment can occur and, together with the topoisomerase II structure, suggests a pathway by which the T segment can be released through the second gate of the enzyme. Mutations that confer resistance to the quinolone antibacterial agents cluster at the new dimer interface, indicating how these drugs might interact with the gyrase-DNA complex.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 a, b, Orthogonal views of GyrA59 and the yeast topo II A' subunit. Head fragments are shown in blue, helix-turn-helix motifs in yellow ( 3) and red ( 4), tail domains in grey, active-site tyrosines as green spheres. Arrows show the direction of movement from topo II to gyrase. c, Opening of the 'second gate' in the primary dimer interface (see text). The A' subunits of yeast topo II were superimposed onto the GyrA59 dimer structure by least-squares fits onto the 'head' fragments. The view is rotated about a vertical axis to show the full extent of the gate ( 22 ?). d, Two conformations of the connecting helices, superimposed at the 'primary' dimer interface. Arrows show the direction of movement from topo II to gyrase. 		Figure 3.
Figure 3 a, GRASP22 electrostatic surface potential of the GyrA59 dimer (orthogonal stereo views).: negatively charged surfaces are in red, positively charged surfaces in blue. The DNA backbone is shown as a green and red ribbon; active-site tyrosines as yellow stars, target phosphoryl groups as yellow dots. b, Close-up of the 'head' dimer interface (colour scheme as in Fig. 2), with some secondary structure elements indicated. Quinolone-resistance sites are shown as numbered black spheres. c, Space-filling model, viewed as in b. Monomers are shown in pale green and pink. Quinolone-resistance sites are in black. Residues picked out in other colours are highly conserved within the topoisomerase family.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1997, 388, 903-906) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23022727 B.H.Schmidt, N.Osheroff, and J.M.Berger (2012).
Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity.
  Nat Struct Mol Biol, 19, 1147-1154.
PDB code: 4gfh
21428949 D.Klostermeier (2011).
Single-molecule FRET reveals nucleotide-driven conformational changes in molecular machines and their link to RNA unwinding and DNA supercoiling.
  Biochem Soc Trans, 39, 611-616.  
20870749 N.M.Baker, S.Weigand, S.Maar-Mathias, and A.Mondragón (2011).
Solution structures of DNA-bound gyrase.
  Nucleic Acids Res, 39, 755-766.  
20738404 S.Heeb, M.P.Fletcher, S.R.Chhabra, S.P.Diggle, P.Williams, and M.Cámara (2011).
Quinolones: from antibiotics to autoinducers.
  FEMS Microbiol Rev, 35, 247-274.  
21227918 X.Xiong, E.H.Bromley, P.Oelschlaeger, D.N.Woolfson, and J.Spencer (2011).
Structural insights into quinolone antibiotic resistance mediated by pentapeptide repeat proteins: conserved surface loops direct the activity of a Qnr protein from a Gram-negative bacterium.
  Nucleic Acids Res, 39, 3917-3927.
PDB codes: 3pss 3psz
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
20686482 B.D.Bax, P.F.Chan, D.S.Eggleston, A.Fosberry, D.R.Gentry, F.Gorrec, I.Giordano, M.M.Hann, A.Hennessy, M.Hibbs, J.Huang, E.Jones, J.Jones, K.K.Brown, C.J.Lewis, E.W.May, M.R.Saunders, O.Singh, C.E.Spitzfaden, C.Shen, A.Shillings, A.J.Theobald, A.Wohlkonig, N.D.Pearson, and M.N.Gwynn (2010).
Type IIA topoisomerase inhibition by a new class of antibacterial agents.
  Nature, 466, 935-940.
PDB codes: 2xco 2xcq 2xcr 2xcs 2xct
20485342 B.H.Schmidt, A.B.Burgin, J.E.Deweese, N.Osheroff, and J.M.Berger (2010).
A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases.
  Nature, 465, 641-644.
PDB codes: 3l4j 3l4k
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.  
20438350 I.Vranakis, V.Sandalakis, D.Chochlakis, Y.Tselentis, and A.Psaroulaki (2010).
DNA gyrase and topoisomerase IV mutations in an in vitro fluoroquinolone-resistant Coxiella burnetii strain.
  Microb Drug Resist, 16, 111-117.  
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
20952390 J.Yuan, Y.Sterckx, L.A.Mitchenall, A.Maxwell, R.Loris, and M.K.Waldor (2010).
Vibrio cholerae ParE2 poisons DNA gyrase via a mechanism distinct from other gyrase inhibitors.
  J Biol Chem, 285, 40397-40408.  
20440275 M.A.Kohanski, D.J.Dwyer, and J.J.Collins (2010).
How antibiotics kill bacteria: from targets to networks.
  Nat Rev Microbiol, 8, 423-435.  
20127325 P.Xie (2010).
Dynamics of strand passage catalyzed by topoisomerase II.
  Eur Biophys J, 39, 1251-1259.  
20932305 Q.Guo, J.Weng, X.Xu, M.Wang, X.Wang, X.Ye, W.Wang, and M.Wang (2010).
A mutational analysis and molecular dynamics simulation of quinolone resistance proteins QnrA1 and QnrC from Proteus mirabilis.
  BMC Struct Biol, 10, 33.  
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.  
19060136 A.Mérens, S.Matrat, A.Aubry, C.Lascols, V.Jarlier, C.J.Soussy, J.D.Cavallo, and E.Cambau (2009).
The pentapeptide repeat proteins MfpAMt and QnrB4 exhibit opposite effects on DNA gyrase catalytic reactions and on the ternary gyrase-DNA-quinolone complex.
  J Bacteriol, 191, 1587-1594.  
  19342777 G.Fu, J.Wu, D.Zhu, Y.Hu, L.Bi, X.E.Zhang, and d.a. .C.Wang (2009).
Crystallization and preliminary crystallographic studies of Mycobacterium tuberculosis DNA gyrase B C-terminal domain, part of the enzyme reaction core.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 350-352.  
19596812 G.Fu, J.Wu, W.Liu, D.Zhu, Y.Hu, J.Deng, X.E.Zhang, L.Bi, and D.C.Wang (2009).
Crystal structure of DNA gyrase B' domain sheds lights on the mechanism for T-segment navigation.
  Nucleic Acids Res, 37, 5908-5916.
PDB code: 2zjt
19281311 L.Nguyen, and J.Pieters (2009).
Mycobacterial subversion of chemotherapeutic reagents and host defense tactics: challenges in tuberculosis drug development.
  Annu Rev Pharmacol Toxicol, 49, 427-453.  
19965760 M.J.Edwards, R.H.Flatman, L.A.Mitchenall, C.E.Stevenson, T.B.Le, T.A.Clarke, A.R.McKay, H.P.Fiedler, M.J.Buttner, D.M.Lawson, and A.Maxwell (2009).
A crystal structure of the bifunctional antibiotic simocyclinone d8, bound to DNA gyrase.
  Science, 326, 1415-1418.
PDB codes: 2wl2 2y3p
19273669 M.L.Beeton, V.J.Chalker, N.C.Maxwell, S.Kotecha, and O.B.Spiller (2009).
Concurrent titration and determination of antibiotic resistance in ureaplasma species with identification of novel point mutations in genes associated with resistance.
  Antimicrob Agents Chemother, 53, 2020-2027.  
19465484 M.Simic, N.De Jonge, R.Loris, G.Vesnaver, and J.Lah (2009).
Driving forces of gyrase recognition by the addiction toxin CcdB.
  J Biol Chem, 284, 20002-20010.  
19647513 N.De Jonge, A.Garcia-Pino, L.Buts, S.Haesaerts, D.Charlier, K.Zangger, L.Wyns, H.De Greve, and R.Loris (2009).
Rejuvenation of CcdB-poisoned gyrase by an intrinsically disordered protein domain.
  Mol Cell, 35, 154-163.
PDB codes: 3g7z 3hpw
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.  
17724149 K.Drlica, M.Malik, R.J.Kerns, and X.Zhao (2008).
Quinolone-mediated bacterial death.
  Antimicrob Agents Chemother, 52, 385-392.  
18160515 L.Balsalobre, and A.G.de la Campa (2008).
Fitness of Streptococcus pneumoniae fluoroquinolone-resistant strains with topoisomerase IV recombinant genes.
  Antimicrob Agents Chemother, 52, 822-830.  
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.  
18268084 S.M.Hashimi, G.Huang, A.Maxwell, and R.G.Birch (2008).
DNA gyrase from the albicidin producer Xanthomonas albilineans has multiple-antibiotic-resistance and unusual enzymatic properties.
  Antimicrob Agents Chemother, 52, 1382-1390.  
18426901 S.Matrat, A.Aubry, C.Mayer, V.Jarlier, and E.Cambau (2008).
Mutagenesis in the alpha3alpha4 GyrA helix and in the Toprim domain of GyrB refines the contribution of Mycobacterium tuberculosis DNA gyrase to intrinsic resistance to quinolones.
  Antimicrob Agents Chemother, 52, 2909-2914.  
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.  
17682095 D.A.Ostrov, J.A.Hernández Prada, P.E.Corsino, K.A.Finton, N.Le, and T.C.Rowe (2007).
Discovery of novel DNA gyrase inhibitors by high-throughput virtual screening.
  Antimicrob Agents Chemother, 51, 3688-3698.  
17517767 F.Mueller-Planitz, and D.Herschlag (2007).
DNA topoisomerase II selects DNA cleavage sites based on reactivity rather than binding affinity.
  Nucleic Acids Res, 35, 3764-3773.  
17375187 I.Laponogov, D.A.Veselkov, M.K.Sohi, X.S.Pan, A.Achari, C.Yang, J.D.Ferrara, L.M.Fisher, and M.R.Sanderson (2007).
Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target.
  PLoS ONE, 2, e301.
PDB code: 2nov
17284163 J.Lipfert, and S.Doniach (2007).
Small-angle X-ray scattering from RNA, proteins, and protein complexes.
  Annu Rev Biophys Biomol Struct, 36, 307-327.  
18097402 K.C.Dong, and J.M.Berger (2007).
Structural basis for gate-DNA recognition and bending by type IIA topoisomerases.
  Nature, 450, 1201-1205.
PDB code: 2rgr
17400739 K.Champion, and N.P.Higgins (2007).
Growth rate toxicity phenotypes and homeostatic supercoil control differentiate Escherichia coli from Salmonella enterica serovar Typhimurium.
  J Bacteriol, 189, 5839-5849.  
17603498 K.D.Corbett, P.Benedetti, and J.M.Berger (2007).
Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI.
  Nat Struct Mol Biol, 14, 611-619.
PDB code: 2q2e
17333143 L.Cao, H.Lin, and V.M.Mirsky (2007).
Detection of antibiotics in food: extraction of fluoroquinolones by DNA.
  Anal Bioanal Chem, 388, 253-258.  
17355868 L.Costenaro, J.G.Grossmann, C.Ebel, and A.Maxwell (2007).
Modular structure of the full-length DNA gyrase B subunit revealed by small-angle X-ray scattering.
  Structure, 15, 329-339.  
17194844 Y.Maeda, A.Kiba, K.Ohnishi, and Y.Hikichi (2007).
Amino acid substitutions in GyrA of Burkholderia glumae are implicated in not only oxolinic acid resistance but also fitness on rice plants.
  Appl Environ Microbiol, 73, 1114-1119.  
16377674 A.Aubry, N.Veziris, E.Cambau, C.Truffot-Pernot, V.Jarlier, and L.M.Fisher (2006).
Novel gyrase mutations in quinolone-resistant and -hypersusceptible clinical isolates of Mycobacterium tuberculosis: functional analysis of mutant enzymes.
  Antimicrob Agents Chemother, 50, 104-112.  
16963775 A.B.Smith, and A.Maxwell (2006).
A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site.
  Nucleic Acids Res, 34, 4667-4676.  
17008172 A.Robicsek, G.A.Jacoby, and D.C.Hooper (2006).
The worldwide emergence of plasmid-mediated quinolone resistance.
  Lancet Infect Dis, 6, 629-640.  
16585773 G.E.Schmitz, and D.M.Downs (2006).
An allele of gyrA prevents Salmonella enterica serovar Typhimurium from using succinate as a carbon source.
  J Bacteriol, 188, 3126-3129.  
  17142909 G.W.Buchko, H.Robinson, S.Ni, H.B.Pakrasi, and M.A.Kennedy (2006).
Cloning, expression, crystallization and preliminary crystallographic analysis of a pentapeptide-repeat protein (Rfr23) from the bacterium Cyanothece 51142.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1251-1254.  
17075135 G.W.Buchko, S.Ni, H.Robinson, E.A.Welsh, H.B.Pakrasi, and M.A.Kennedy (2006).
Characterization of two potentially universal turn motifs that shape the repeated five-residues fold--crystal structure of a lumenal pentapeptide repeat protein from Cyanothece 51142.
  Protein Sci, 15, 2579-2595.
PDB codes: 2f3l 2g0y
16436716 J.Strahilevitz, A.Robicsek, and D.C.Hooper (2006).
Role of the extended alpha4 domain of Staphylococcus aureus gyrase A protein in determining low sensitivity to quinolones.
  Antimicrob Agents Chemother, 50, 600-606.  
16803589 M.Malik, X.Zhao, and K.Drlica (2006).
Lethal fragmentation of bacterial chromosomes mediated by DNA gyrase and quinolones.
  Mol Microbiol, 61, 810-825.  
16385052 M.Oram, A.A.Travers, A.J.Howells, A.Maxwell, and M.L.Pato (2006).
Dissection of the bacteriophage Mu strong gyrase site (SGS): significance of the SGS right arm in Mu biology and DNA gyrase mechanism.
  J Bacteriol, 188, 619-632.  
16388575 M.W.Vetting, S.S.Hegde, J.E.Fajardo, A.Fiser, S.L.Roderick, H.E.Takiff, and J.S.Blanchard (2006).
Pentapeptide repeat proteins.
  Biochemistry, 45, 1.  
  17077506 S.B.Carr, G.Makris, S.E.Phillips, and C.D.Thomas (2006).
Crystallization and preliminary X-ray diffraction analysis of two N-terminal fragments of the DNA-cleavage domain of topoisomerase IV from Staphylococcus aureus.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1164-1167.  
17015625 S.Matrat, N.Veziris, C.Mayer, V.Jarlier, C.Truffot-Pernot, J.Camuset, E.Bouvet, E.Cambau, and A.Aubry (2006).
Functional analysis of DNA gyrase mutant enzymes carrying mutations at position 88 in the A subunit found in clinical strains of Mycobacterium tuberculosis resistant to fluoroquinolones.
  Antimicrob Agents Chemother, 50, 4170-4173.  
16614448 S.N.Richter, E.Leo, G.Giaretta, B.Gatto, L.M.Fisher, and M.Palumbo (2006).
Clerocidin interacts with the cleavage complex of Streptococcus pneumoniae topoisomerase IV to induce selective irreversible DNA damage.
  Nucleic Acids Res, 34, 1982-1991.  
16421857 U.Neugebauer, U.Schmid, K.Baumann, U.Holzgrabe, W.Ziebuhr, S.Kozitskaya, W.Kiefer, M.Schmitt, and J.Popp (2006).
Characterization of bacterial growth and the influence of antibiotics by means of UV resonance Raman spectroscopy.
  Biopolymers, 82, 306-311.  
17038336 Y.Y.Huang, J.Y.Deng, J.Gu, Z.P.Zhang, A.Maxwell, L.J.Bi, Y.Y.Chen, Y.F.Zhou, Z.N.Yu, and X.E.Zhang (2006).
The key DNA-binding residues in the C-terminal domain of Mycobacterium tuberculosis DNA gyrase A subunit (GyrA).
  Nucleic Acids Res, 34, 5650-5659.  
16166547 A.B.Blanc-Potard, G.Labesse, N.Figueroa-Bossi, and L.Bossi (2005).
Mutation at the "exit gate" of the salmonella gyrase a subunit suppresses a defect in the gyrase B subunit.
  J Bacteriol, 187, 6841-6844.  
15897198 A.J.Ruthenburg, D.M.Graybosch, J.C.Huetsch, and G.L.Verdine (2005).
A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias.
  J Biol Chem, 280, 26177-26184.
PDB code: 1zi0
15659402 E.Leo, K.A.Gould, X.S.Pan, G.Capranico, M.R.Sanderson, M.Palumbo, and L.M.Fisher (2005).
Novel symmetric and asymmetric DNA scission determinants for Streptococcus pneumoniae topoisomerase IV and gyrase are clustered at the DNA breakage site.
  J Biol Chem, 280, 14252-14263.  
15760423 F.Van Bambeke, J.M.Michot, J.Van Eldere, and P.M.Tulkens (2005).
Quinolones in 2005: an update.
  Clin Microbiol Infect, 11, 256-280.  
15942878 G.A.Jacoby (2005).
Mechanisms of resistance to quinolones.
  Clin Infect Dis, 41, S120-S126.  
16100112 H.Wei, A.J.Ruthenburg, S.K.Bechis, and G.L.Verdine (2005).
Nucleotide-dependent domain movement in the ATPase domain of a human type IIA DNA topoisomerase.
  J Biol Chem, 280, 37041-37047.
PDB codes: 1zxm 1zxn
16539034 I.C.Romero, N.G.Saravia, and J.Walker (2005).
Selective action of fluoroquinolones against intracellular amastigotes of Leishmania (Viannia) panamensis in vitro.
  J Parasitol, 91, 1474-1479.  
15855486 J.M.Sierra, L.Martinez-Martinez, F.Vázquez, E.Giralt, and J.Vila (2005).
Relationship between mutations in the gyrA gene and quinolone resistance in clinical isolates of Corynebacterium striatum and Corynebacterium amycolatum.
  Antimicrob Agents Chemother, 49, 1714-1719.  
16126848 K.Siegmund, S.Maheshwary, S.Narayanan, W.Connors, M.Riedrich, M.Printz, and C.Richert (2005).
Molecular details of quinolone-DNA interactions: solution structure of an unusually stable DNA duplex with covalently linked nalidixic acid residues and non-covalent complexes derived from it.
  Nucleic Acids Res, 33, 4838-4848.
PDB code: 2bq2
15698572 L.Costenaro, J.G.Grossmann, C.Ebel, and A.Maxwell (2005).
Small-angle X-ray scattering reveals the solution structure of the full-length DNA gyrase a subunit.
  Structure, 13, 287-296.  
16314322 L.Sari, and I.Andricioaei (2005).
Rotation of DNA around intact strand in human topoisomerase I implies distinct mechanisms for positive and negative supercoil relaxation.
  Nucleic Acids Res, 33, 6621-6634.  
15933203 S.S.Hegde, M.W.Vetting, S.L.Roderick, L.A.Mitchenall, A.Maxwell, H.E.Takiff, and J.S.Blanchard (2005).
A fluoroquinolone resistance protein from Mycobacterium tuberculosis that mimics DNA.
  Science, 308, 1480-1483.
PDB codes: 2bm4 2bm5 2bm6 2bm7
15930158 U.H.Manjunatha, A.Maxwell, and V.Nagaraja (2005).
A monoclonal antibody that inhibits mycobacterial DNA gyrase by a novel mechanism.
  Nucleic Acids Res, 33, 3085-3094.  
16267301 Z.Pang, R.Chen, D.Manna, and N.P.Higgins (2005).
A gyrase mutant with low activity disrupts supercoiling at the replication terminus.
  J Bacteriol, 187, 7773-7783.  
15388925 A.Korostelev, M.O.Fenley, and M.S.Chapman (2004).
Impact of a Poisson-Boltzmann electrostatic restraint on protein structures refined at medium resolution.
  Acta Crystallogr D Biol Crystallogr, 60, 1786-1794.  
14742217 E.S.Pfeiffer, and H.Hiasa (2004).
Replacement of ParC alpha4 helix with that of GyrA increases the stability and cytotoxicity of topoisomerase IV-quinolone-DNA ternary complexes.
  Antimicrob Agents Chemother, 48, 608-611.  
15047688 J.Roca (2004).
The path of the DNA along the dimer interface of topoisomerase II.
  J Biol Chem, 279, 25783-25788.  
15037624 J.V.Walker, K.C.Nitiss, L.H.Jensen, C.Mayne, T.Hu, P.B.Jensen, M.Sehested, T.Hsieh, and J.L.Nitiss (2004).
A mutation in human topoisomerase II alpha whose expression is lethal in DNA repair-deficient yeast cells.
  J Biol Chem, 279, 25947-25954.  
15155208 K.A.Gould, X.S.Pan, R.J.Kerns, and L.M.Fisher (2004).
Ciprofloxacin dimers target gyrase in Streptococcus pneumoniae.
  Antimicrob Agents Chemother, 48, 2108-2115.  
15139806 K.D.Corbett, and J.M.Berger (2004).
Structure, molecular mechanisms, and evolutionary relationships in DNA topoisomerases.
  Annu Rev Biophys Biomol Struct, 33, 95.  
15123801 K.D.Corbett, R.K.Shultzaberger, and J.M.Berger (2004).
The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold.
  Proc Natl Acad Sci U S A, 101, 7293-7298.
PDB code: 1suu
15159578 M.H.Dao-Thi, L.Van Melderen, E.De Genst, L.Buts, A.Ranquin, L.Wyns, and R.Loris (2004).
Crystallization of CcdB in complex with a GyrA fragment.
  Acta Crystallogr D Biol Crystallogr, 60, 1132-1134.  
15026536 N.Suda, Y.Ito, T.Imai, T.Kikumori, A.Kikuchi, Y.Nishiyama, S.Yoshida, and M.Suzuki (2004).
The alpha4 residues of human DNA topoisomerase IIalpha function in enzymatic activity and anticancer drug sensitivity.
  Nucleic Acids Res, 32, 1767-1773.  
14993694 T.J.Hsieh, and N.L.Chan (2004).
Crystallization and preliminary X-ray crystallographic analysis of the C-terminal domain of ParC protein from Bacillus stearothermophilus.
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15345450 Y.Maeda, A.Kiba, K.Ohnishi, and Y.Hikichi (2004).
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12604512 C.G.Noble, F.M.Barnard, and A.Maxwell (2003).
Quinolone-DNA interaction: sequence-dependent binding to single-stranded DNA reflects the interaction within the gyrase-DNA complex.
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12499202 D.Ince, X.Zhang, L.C.Silver, and D.C.Hooper (2003).
Topoisomerase targeting with and resistance to gemifloxacin in Staphylococcus aureus.
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12878515 D.R.Macinga, P.J.Renick, K.M.Makin, D.H.Ellis, A.A.Kreiner, M.Li, K.J.Rupnik, E.M.Kincaid, C.D.Wallace, B.Ledoussal, and T.W.Morris (2003).
Unique biological properties and molecular mechanism of 5,6-bridged quinolones.
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14527324 G.L.Verdine, and D.P.Norman (2003).
Covalent trapping of protein-DNA complexes.
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14507384 M.Oram, A.J.Howells, A.Maxwell, and M.L.Pato (2003).
A biochemical analysis of the interaction of DNA gyrase with the bacteriophage Mu, pSC101 and pBR322 strong gyrase sites: the role of DNA sequence in modulating gyrase supercoiling and biological activity.
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12519191 T.D.Sokolsky, and T.A.Baker (2003).
DNA gyrase requirements distinguish the alternate pathways of Mu transposition.
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12183223 D.Strumberg, J.L.Nitiss, J.Dong, J.Walker, M.C.Nicklaus, K.W.Kohn, J.G.Heddle, A.Maxwell, S.Seeber, and Y.Pommier (2002).
Importance of the fourth alpha-helix within the CAP homology domain of type II topoisomerase for DNA cleavage site recognition and quinolone action.
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12021440 F.Fabiola, R.Bertram, A.Korostelev, and M.S.Chapman (2002).
An improved hydrogen bond potential: impact on medium resolution protein structures.
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Quinolone-binding pocket of DNA gyrase: role of GyrB.
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12007640 L.J.Piddock (2002).
Fluoroquinolone resistance in Salmonella serovars isolated from humans and food animals.
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11741897 M.H.Dao-Thi, D.Charlier, R.Loris, D.Maes, J.Messens, L.Wyns, and J.Backmann (2002).
Intricate interactions within the ccd plasmid addiction system.
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11948793 M.J.Romanowski, S.A.Gibney, and S.K.Burley (2002).
Crystal structure of the Escherichia coli SbmC protein that protects cells from the DNA replication inhibitor microcin B17.
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PDB code: 1jyh
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A GyrB-GyrA fusion protein expressed in yeast cells is able to remove DNA supercoils but cannot substitute eukaryotic topoisomerase II.
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11850422 V.Lamour, L.Hoermann, J.M.Jeltsch, P.Oudet, and D.Moras (2002).
An open conformation of the Thermus thermophilus gyrase B ATP-binding domain.
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PDB code: 1kij
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C-terminal domain of gyrase A is predicted to have a beta-propeller structure.
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11248029 A.V.Vologodskii, W.Zhang, V.V.Rybenkov, A.A.Podtelezhnikov, D.Subramanian, J.D.Griffith, and N.R.Cozzarelli (2001).
Mechanism of topology simplification by type II DNA topoisomerases.
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New mutation in parE in a pneumococcal in vitro mutant resistant to fluoroquinolones.
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Mechanisms of action of antimicrobials: focus on fluoroquinolones.
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Emerging mechanisms of fluoroquinolone resistance.
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Mechanisms and frequency of resistance to gatifloxacin in comparison to AM-1121 and ciprofloxacin in Staphylococcus aureus.
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Quinolone Resistance: Older Concepts and Newer Developments.
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11395412 J.J.Champoux (2001).
DNA topoisomerases: structure, function, and mechanism.
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11266562 J.Mrázek, D.Bhaya, A.R.Grossman, and S.Karlin (2001).
Highly expressed and alien genes of the Synechocystis genome.
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DNA gyrase-mediated natural resistance to fluoroquinolones in Ehrlichia spp.
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11245203 R.Marchetto, E.Nicolás, N.Castillo, J.Bacardit, M.Navia, J.Vila, and E.Giralt (2001).
Two short peptides including segments of subunit A of Escherichia coli DNA gyrase as potential probes to evaluate the antibacterial activity of quinolones.
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11557482 S.Hartman-Neumann, K.DenBleyker, L.A.Pelosi, L.E.Lawrence, J.F.Barrett, and T.J.Dougherty (2001).
Selection and genetic characterization of Streptococcus pneumoniae mutants resistant to the des-F(6) quinolone BMS-284756.
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Mechanisms and frequency of resistance to premafloxacin in Staphylococcus aureus: novel mutations suggest novel drug-target interactions.
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Mutagenesis of E477 or K505 in the B' domain of human topoisomerase II beta increases the requirement for magnesium ions during strand passage.
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The 2-pyridone antibacterial agents: bacterial topoisomerase inhibitors.
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Crystal structure of a Flp recombinase-Holliday junction complex: assembly of an active oligomer by helix swapping.
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PDB code: 1flo
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Position-specific trapping of topoisomerase I-DNA cleavage complexes by intercalated benzo[a]- pyrene diol epoxide adducts at the 6-amino group of adenine.
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Topoisomerase II drives DNA transport by hydrolyzing one ATP.
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Addiction modules and programmed cell death and antideath in bacterial cultures.
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NMR structure of the N-terminal domain of E. coli DnaB helicase: implications for structure rearrangements in the helicase hexamer.
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Mechanism of fluoroquinolone action.
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Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11.
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Locking the DNA gate of DNA gyrase: investigating the effects on DNA cleavage and ATP hydrolysis.
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A model for the mechanism of strand passage by DNA gyrase.
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Probing the binding of coumarins and cyclothialidines to DNA gyrase.
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Yeast topoisomerase II is inhibited by etoposide after hydrolyzing the first ATP and before releasing the second ADP.
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Identification of a residue involved in transition-state stabilization in the ATPase reaction of DNA gyrase.
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Molecular characterization of the gene encoding the DNA gyrase A subunit of Streptococcus pneumoniae.
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Correlation between quinolone susceptibility patterns and sequences in the A and B subunits of DNA gyrase in mycobacteria.
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Structural similarities between topoisomerases that cleave one or both DNA strands.
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Type II DNA topoisomerases.
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Bacteriophage T4, a model system for understanding the mechanism of type II topoisomerase inhibitors.
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Bacterial death by DNA gyrase poisoning.
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A mutant yeast topoisomerase II (top2G437S) with differential sensitivity to anticancer drugs in the presence and absence of ATP.
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Inhibitory activities of gatifloxacin (AM-1155), a newly developed fluoroquinolone, against bacterial and mammalian type II topoisomerases.
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Quinolone resistance mutations in the GrlB protein of Staphylococcus aureus.
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Identification of active site residues in the "GyrA" half of yeast DNA topoisomerase II.
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Conformational changes in DNA gyrase revealed by limited proteolysis.
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The DNA gyrase-quinolone complex. ATP hydrolysis and the mechanism of DNA cleavage.
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9545289 T.Hu, S.Chang, and T.Hsieh (1998).
Identifying Lys359 as a critical residue for the ATP-dependent reactions of Drosophila DNA topoisomerase II.
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Protein-nucleic acid interactions.
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Pre-steady-state analysis of ATP hydrolysis by Saccharomyces cerevisiae DNA topoisomerase II. 2. Kinetic mechanism for the sequential hydrolysis of two ATP.
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DNA gyrase and topoisomerase IV are dual targets of clinafloxacin action in Streptococcus pneumoniae.
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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.

 

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