A unique 45-amino-acid region in the toprim domain of Plasmodium falciparum gyrase B is essential for its activity.
DNA gyrase is the only topoisomerase that can introduce negative supercoils into the DNA at the cost of ATP hydrolysis. Some but not all the steps of the topoisomerization reaction are understood clearly for both eukaryotic topoII and DNA gyrase. This study is an attempt to understand whether the B subunit of DNA gyrase binds to DNA directly, which may be central to the stimulation of its ATPase activity essential for gyrase function. We have dissected the Plasmodium falciparum gyrase B (PfGyrB) subunit to identify a 45-amino-acid region in the toprim domain that is responsible for its intrinsic DNA binding activity, DNA-stimulated ATPase activity, and DNA cleavage. We find that DNA has to enter through the ATP-operated clamp of PfGyrB to gain access to the DNA binding region. Furthermore, the rate of ATP hydrolysis of PfGyrB increases significantly with increasing DNA length, suggesting a possible communication between the ATPase domain and the DNA binding region that can account for its optimal ATPase activity. These results not only highlight the mechanism of GyrB action in the deadly human parasite P. falciparum but also provide meaningful insights into the current mechanistic model of DNA transport by gyrase during the topoisomerization reaction.
Dar
Ashraf
A
Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India.
Prusty
Dhaneswar
D
Mondal
Neelima
N
Dhar
Suman K
SK
D000595:Amino Acid Sequence; D027081:DNA Gyrase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D010963:Plasmodium falciparum / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics; D017434:Protein Structure, Tertiary; D021122:Protein Subunits / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015800:Protozoan Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D016415:Sequence Alignment
D021122:Protein Subunits; D015800:Protozoan Proteins; D027081:DNA Gyrase
Mol Biochem Parasitol. 2007 Jul;154(1):30-9
17499371
Biochemistry. 1993 Mar 16;32(10):2717-24
8383523
J Mol Biol. 2001 Mar 9;306(5):969-84
11237612
J Biol Chem. 1996 Apr 19;271(16):9723-9
8621650
J Mol Biol. 1996 Aug 16;261(2):155-72
8757284
J Biol Chem. 2002 Aug 30;277(35):31310-7
12045190
Eukaryot Cell. 2007 Mar;6(3):398-412
17220464
Nucleic Acids Res. 2006;34(19):5650-9
17038336
Mol Biochem Parasitol. 2005 Mar;140(1):107-17
15694492
Proc Natl Acad Sci U S A. 1996 Dec 10;93(25):14416-21
8962066
Protein Eng. 1992 Apr;5(3):191-5
1409538
Nucleic Acids Res. 1991 Apr 11;19(7):1399-405
1851291
Structure. 2007 Mar;15(3):329-39
17355868
Nucleic Acids Res. 1991 May 25;19(10):2785
1645866
Nature. 1991 Jun 20;351(6328):624-9
1646964
Cell. 2003 Dec 26;115(7):771-85
14697197
J Biol Chem. 1997 Dec 19;272(51):32696-703
9405488
J Biol Chem. 1999 Jul 30;274(31):21688-94
10419479
Nucleic Acids Res. 1998 Sep 15;26(18):4205-13
9722641
Nat Protoc. 2007;2(4):924-32
17446874
Annu Rev Biophys Biomol Struct. 2004;33:95-118
15139806
J Biol Chem. 1991 Apr 15;266(11):6659-62
1849888
J Biol Chem. 2000 Apr 28;275(17):13041-8
10777608
Annu Rev Biochem. 2001;70:369-413
11395412
Nucleic Acids Res. 2007;35(9):2861-74
17430964
Proc Natl Acad Sci U S A. 1976 Nov;73(11):3872-6
186775
Mol Biochem Parasitol. 2003 Jan;126(1):9-14
12554079
J Biol Chem. 1989 Nov 25;264(33):19648-53
2555327
J Biol Chem. 2006 Aug 18;281(33):23395-404
16782968
Nature. 2007 Dec 20;450(7173):1201-5
18097402
J Biol Chem. 2002 Feb 22;277(8):5944-51
11850431
J Biol Chem. 1980 Jul 10;255(13):6299-306
6248518
Proc Natl Acad Sci U S A. 1979 Dec;76(12):6289-93
230505
Nat Protoc. 2006;1(6):2876-90
17406547
Nat Protoc. 2007;2(8):1849-61
17703195
Proc Natl Acad Sci U S A. 2007 Mar 20;104(12):4773-4
17363472
Nucleic Acids Res. 1984 Jan 25;12(2):901-14
6198633
Nucleic Acids Res. 1996 Dec 15;24(24):4868-73
9016655
J Biol Chem. 2000 Jul 28;275(30):22888-94
10764756
Nat Struct Mol Biol. 2007 Apr;14(4):264-71
17334374
Nucleic Acids Res. 2009 Feb;37(3):721-30
19059997
Cell. 1992 Nov 27;71(5):833-40
1330327