title: Structural study and thermodynamic characterization of inhibitor binding to lumazine synthase from Bacillus anthracis.
abstract: The crystal structure of lumazine synthase from Bacillus anthracis was solved by molecular replacement and refined to R(cryst) = 23.7% (R(free) = 28.4%) at a resolution of 3.5 A. The structure reveals the icosahedral symmetry of the enzyme and specific features of the active site that are unique in comparison with previously determined orthologues. The application of isothermal titration calorimetry in combination with enzyme kinetics showed that three designed pyrimidine derivatives bind to lumazine synthase with micromolar dissociation constants and competitively inhibit the catalytic reaction. Structure-based modelling suggested the binding modes of the inhibitors in the active site and allowed an estimation of the possible contacts formed upon binding. The results provide a structural framework for the design of antibiotics active against B. anthracis.
authors.affiliation: Karolinska Institutet NOVUM, Center of Structural Biochemistry, Huddinge, Sweden.
authors.forename: Ekaterina
authors.initials: E
authors.lastname: Morgunova
authors.forename: Boris
authors.initials: B
authors.lastname: Illarionov
authors.forename: Sabine
authors.initials: S
authors.lastname: Saller
authors.forename: Aleksander
authors.initials: A
authors.lastname: Popov
authors.forename: Thota
authors.initials: T
authors.lastname: Sambaiah
authors.forename: Adelbert
authors.initials: A
authors.lastname: Bacher
authors.forename: Mark
authors.initials: M
authors.lastname: Cushman
authors.forename: Markus
authors.initials: M
authors.lastname: Fischer
authors.forename: Rudolf
authors.initials: R
authors.lastname: Ladenstein
mesh_terms: D000595:Amino Acid Sequence; D001408:Bacillus anthracis / Q000201:enzymology*; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009097:Multienzyme Complexes / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D013379:Substrate Specificity; D013816:Thermodynamics
chemical_list: D004791:Enzyme Inhibitors; D009097:Multienzyme Complexes; C044822:6,7-dimethyl-8-ribityllumazine synthase
references.citation: J Mol Biol. 2000 Apr 14;297(5):1031-6
references.pmid: 10764570
references.citation: J Org Chem. 2005 Sep 30;70(20):8162-70
references.pmid: 16277343
references.citation: Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21
references.pmid: 9757107
references.citation: Anal Biochem. 2005 Mar 1;338(1):124-30
references.pmid: 15707942
references.citation: J Mol Biol. 2000 May 26;299(1):181-97
references.pmid: 10860731
references.citation: J Org Chem. 2008 Apr 4;73(7):2715-24
references.pmid: 18331058
references.citation: Protein Sci. 1999 Nov;8(11):2355-65
references.pmid: 10595538
references.citation: Biochemistry. 1995 Mar 7;34(9):2883-92
references.pmid: 7893702
references.citation: Acta Crystallogr A. 1991 Mar 1;47 ( Pt 2):110-9
references.pmid: 2025413
references.citation: J Biol Chem. 2007 Jun 8;282(23):17231-41
references.pmid: 17446177
references.citation: Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54
references.pmid: 12393927
references.citation: Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):58-64
references.pmid: 16369094
references.citation: J Org Chem. 2004 Feb 6;69(3):601-12
references.pmid: 14750781
references.citation: J Mol Biol. 2001 Mar 9;306(5):1099-114
references.pmid: 11237620
references.citation: J Mol Biol. 2002 May 17;318(5):1317-29
references.pmid: 12083520
references.citation: J Org Chem. 2002 Aug 9;67(16):5807-16
references.pmid: 12153285
references.citation: Biochemistry. 2005 Mar 1;44(8):2746-58
references.pmid: 15723519
references.citation: J Mol Biol. 1988 Oct 20;203(4):1045-70
references.pmid: 3145341
references.citation: J Comput Chem. 2004 Oct;25(13):1605-12
references.pmid: 15264254
references.citation: J Mol Biol. 2003 Feb 21;326(3):783-93
references.pmid: 12581640
references.citation: J Mol Biol. 1995 Oct 13;253(1):151-67
references.pmid: 7473709
references.citation: Bioorg Med Chem Lett. 1999 Jan 4;9(1):39-42
references.pmid: 9990453
references.citation: J Mol Biol. 2005 Oct 14;353(1):124-37
references.pmid: 16165152
references.citation: J Org Chem. 1999 Jun 25;64(13):4635-4642
references.pmid: 11674533
references.citation: FEBS J. 2006 Oct;273(20):4790-804
references.pmid: 16984393
references.citation: J Biol Chem. 1995 Jul 14;270(28):16788-95
references.pmid: 7622491
references.citation: Nat Struct Biol. 1997 Apr;4(4):269-75
references.pmid: 9095194
references.citation: Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32
references.pmid: 15572765
references.citation: Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125-32
references.pmid: 20124692
references.citation: J Mol Biol. 2003 Apr 18;328(1):167-82
references.pmid: 12684006
references.citation: Anal Biochem. 1996 Jun 1;237(2):260-73
references.pmid: 8660575
references.citation: Structure. 2001 Jan 10;9(1):11-8
references.pmid: 11342130
references.citation: J Mol Graph Model. 2006 Oct;25(2):247-60
references.pmid: 16458552
references.citation: J Org Chem. 2001 Dec 14;66(25):8320-7
references.pmid: 11735509