NORMAL GENOMIC

• Corbett KD, Berger JM
• Structural basis for topoisomerase VI inhibition by the anti-Hsp90 drugradicicol.
• Nucleic Acids Res. 2006; 34: 4269-77
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• Members of the GHL ATPase superfamily, including type II topoisomerases,Hsp90-class chaperones, and MutL, all share a common GHKL-type ATP-bindingfold and act as nucleotide-controlled 'molecular clamps'. These enzymes'ATP-binding sites have proven to be rich drug targets, and certaininhibitors of type II topoisomerases and Hsp90 bind to this region andcompetitively inhibit these enzymes. Recently, it was found thatradicicol, a drug known to block Hsp90 function, also inhibits thearchaeal type IIB topoisomerase topo VI. Here, we use X-raycrystallography to show that despite low sequence identity ( approximately10-12%) between topo VI and Hsp90, radicicol binds to the ATPase sites ofthese two enzymes in an equivalent manner. We further demonstrate thatradicicol inhibits both the dimerization of the topo VI ATPase domains andATP hydrolysis, two critical steps in the enzyme's strand passagereaction. This work contributes to a growing set of structures detailingthe interactions between GHL-family proteins and various drugs, andreveals radicicol as a versatile scaffold for targeting distantly relatedGHL enzymes.

• Corbett KD, Shultzaberger RK, Berger JM
• The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheelfold.
• Proc Natl Acad Sci U S A. 2004; 101: 7293-8
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• DNA gyrase is unique among enzymes for its ability to actively introducenegative supercoils into DNA. This function is mediated in part by theC-terminal domain of its A subunit (GyrA CTD). Here, we report the crystalstructure of this approximately 35-kDa domain determined to 1.75-Aresolution. The GyrA CTD unexpectedly adopts an unusual fold, which weterm a beta-pinwheel, that is globally reminiscent of a beta-propeller butis built of blades with a previously unobserved topology. A large,conserved basic patch on the outer edge of this domain suggests a likelysite for binding and bending DNA; fluorescence resonance energytransfer-based assays show that the GyrA CTD is capable of bending DNA by> or =180 degrees over a 40-bp region. Surprisingly, we find that the CTDof the topoisomerase IV A subunit, which shares limited sequence homologywith the GyrA CTD, also bends DNA. Together, these data provide a physicalexplanation for the ability of DNA gyrase to constrain a positivesuperhelical DNA wrap, and also suggest that the particular substratepreferences of topoisomerase IV might be dictated in part by the functionof this domain.

• Steussy CN, Popov KM, Bowker-Kinley MM, Sloan RB Jr, Harris RA, Hamilton JA
• Structure of pyruvate dehydrogenase kinase. Novel folding pattern for aserine protein kinase.
• J Biol Chem. 2001; 276: 37443-50
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• The structure of mitochondrial pyruvate dehydrogenase kinase isozyme 2 isof interest because it represents a family of serine-specific proteinkinases that lack sequence similarity with all other eukaryotic proteinkinases. Similarity exists instead with key motifs of prokaryotichistidine protein kinases and a family of eukaryotic ATPases. The 2.5-Acrystal structure reported here reveals that pyruvate dehydrogenase kinaseisozyme 2 has two domains of about the same size. The N-terminal half isdominated by a bundle of four amphipathic alpha-helices, whereas theC-terminal half is folded into an alpha/beta sandwich that contains thenucleotide-binding site. Analysis of the structure reveals this C-terminaldomain to be very similar to the nucleotide-binding domain of bacterialhistidine kinases, but the catalytic mechanism appears similar to that ofthe eukaryotic serine kinases and ATPases.

• Maxwell A
• The interaction between coumarin drugs and DNA gyrase.
• Mol Microbiol. 1993; 9: 681-6
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• The coumarin group of antibiotics have as their target the bacterialenzyme DNA gyrase. The drugs bind to the B subunit of gyrase and inhibitDNA supercoiling by blocking the ATPase activity. Recent data show thatthe binding site for the drugs lies within the N-terminal part of the Bprotein, and individual amino acids involved in coumarin interaction arebeing identified. The mode of inhibition of the gyrase ATPase reaction bycoumarins is unlikely to be simple competitive inhibition, and the drugsmay act by stabilizing a conformation of the enzyme with low affinity forATP.

• Brown PO, Cozzarelli NR
• A sign inversion mechanism for enzymatic supercoiling of DNA.
• Science. 1979; 206: 1081-3
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• Both the introduction and the removal of supertwists by DNA gyrase changethe linking number of DNA in steps of two. This surprising findingprovides strong evidence that gyrase acts by a mechanism, called signinversion, whereby a positive supercoil is directly inverted into anegative one via a transient double-strand break.