title: Structural and biochemical characterization of compounds inhibiting Mycobacterium tuberculosis pantothenate kinase.
abstract: Mycobacterium tuberculosis, the bacterial causative agent of tuberculosis, currently affects millions of people. The emergence of drug-resistant strains makes development of new antibiotics targeting the bacterium a global health priority. Pantothenate kinase, a key enzyme in the universal biosynthesis of the essential cofactor CoA, was targeted in this study to find new tuberculosis drugs. The biochemical characterizations of two new classes of compounds that inhibit pantothenate kinase from M. tuberculosis are described, along with crystal structures of their enzyme-inhibitor complexes. These represent the first crystal structures of this enzyme with engineered inhibitors. Both classes of compounds bind in the active site of the enzyme, overlapping with the binding sites of the natural substrate and product, pantothenate and phosphopantothenate, respectively. One class of compounds also interferes with binding of the cofactor ATP. The complexes were crystallized in two crystal forms, one of which is in a new space group for this enzyme and diffracts to the highest resolution reported for any pantothenate kinase structure. These two crystal forms allowed, for the first time, modeling of the cofactor-binding loop in both open and closed conformations. The structures also show a binding mode of ATP different from that previously reported for the M. tuberculosis enzyme but similar to that in the pantothenate kinases of other organisms.
authors: Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, SE-751 24 Uppsala, Sweden. christofer@xray.bmc.uu.se
authors: Christofer
authors: C
authors: Björkelid
authors: Terese
authors: T
authors: Bergfors
authors: Anand Kumar V
authors: AK
authors: Raichurkar
authors: Kakoli
authors: K
authors: Mukherjee
authors: Krishnan
authors: K
authors: Malolanarasimhan
authors: Balachandra
authors: B
authors: Bandodkar
authors: T Alwyn
authors: TA
authors: Jones
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D055162:Biocatalysis / Q000187:drug effects; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009169:Mycobacterium tuberculosis / Q000201:enzymology*; D010205:Pantothenic Acid / Q000031:analogs & derivatives / Q000378:metabolism; D017853:Phosphotransferases (Alcohol Group Acceptor) / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D004791:Enzyme Inhibitors; D010205:Pantothenic Acid; C011988:phosphopantothenic acid; D000255:Adenosine Triphosphate; D017853:Phosphotransferases (Alcohol Group Acceptor); C023088:pantothenate kinase
keywords: CoaA; Coenzyme A; Crystal Structure; Drug Design; Enzyme Inhibitors; Mycobacterium tuberculosis; Pantothenate Kinase
references: Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):235-42
references: 21460441
references: Acta Crystallogr D Biol Crystallogr. 2006 Jun;62(Pt 6):628-38
references: 16699190
references: J Biol Chem. 2005 May 27;280(21):20185-8
references: 15795230
references: Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):48-57
references: 16369093
references: Structure. 1996 Dec 15;4(12):1395-400
references: 8994966
references: J Biol Chem. 2004 Aug 20;279(34):35622-9
references: 15136582
references: J Bacteriol. 1979 Dec;140(3):805-8
references: 230178
references: Acta Crystallogr D Biol Crystallogr. 2001 Aug;57(Pt 8):1201-3
references: 11468417
references: Acta Crystallogr D Biol Crystallogr. 2009 May;65(Pt 5):510-2
references: 19390156
references: Methods Enzymol. 1997;277:525-45
references: 18488323
references: Acta Crystallogr D Biol Crystallogr. 2011 Sep;67(Pt 9):774-83
references: 21904030
references: Microbiology (Reading). 2010 Sep;156(Pt 9):2691-2701
references: 20576686
references: Bioinformatics. 2007 Nov 1;23(21):2947-8
references: 17846036
references: J Biol Chem. 2005 Feb 4;280(5):3314-22
references: 15548531
references: Acta Crystallogr D Biol Crystallogr. 2009 Apr;65(Pt 4):312-25
references: 19307712
references: J Biol Chem. 2000 Sep 8;275(36):28093-9
references: 10862768
references: Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67
references: 21460454
references: Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):72-82
references: 16369096
references: EMBO J. 1982;1(8):945-51
references: 6329717
references: Nat Genet. 2001 Aug;28(4):345-9
references: 11479594
references: J Biomol Screen. 2012 Mar;17(3):293-302
references: 22086722
references: J Bacteriol. 2006 Aug;188(15):5532-40
references: 16855243
references: J Bacteriol. 1981 Dec;148(3):926-32
references: 6796563
references: Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9
references: 2025413
references: J Biol Chem. 1987 Feb 25;262(6):2468-71
references: 3029083
references: Gene. 2002 May 29;291(1-2):35-43
references: 12095677
references: J Biol Chem. 1994 Oct 28;269(43):27051-8
references: 7929447
references: J Clin Microbiol. 1998 Feb;36(2):362-6
references: 9466742
references: J Mol Biol. 2010 Jul 9;400(2):171-85
references: 20451532
references: Science. 2007 Sep 28;317(5846):1881-6
references: 17901324
references: J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674
references: 19461840
references: J Mol Biol. 1968 Apr 28;33(2):491-7
references: 5700707