Untitled - Shodhganga

Bibliography
Adams PO, Afonine PV, Bunko' czi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ,
Grosse-Kunstleve RW, McCoy AJ. Moriarty NW. Oeffner R. Read RJ. Richardson DC, Richardson JS.
Terwilliger TC, Zwart PH. (2010) PHENIX: a comprehensive Python based system for macromolecular
structure solution. Acta. Crystallogr. Sect. D. 66, 213-221.
Ali SN. AI-Khalidi UAS. (1966) The precursor of the xylene ring in riboflavin. Biochem. J. 98. 182-188.
Ananth K, Kumaraswamy S. Narayanaswamy S. Sobhanaditya J. (2003). A conserved domain in prokaryotic
bifunctional FAD synthetase can potentially catalyze nucleotide transfer. Trends Biochem. Sci. 28, 9-12.
Anderson AC. (2003) The process of structure-based drug design. Chem. Bioi. I 0, 787-797.
Andries K, Verhasselt P, Guillemont J, Gohlmann HW, Neefs JM, Winklerm H. VanGestel J, Timmerman P,
Zhu M, Lee E. (2005) A diarylquinoline drug, active on the ATP synthase of Mycobacterium tuberculosis.
Science 307, 223-227.
Arcus VL, Loll JS, Johnston JM, Baker EN. (2006) The potential impact of structural genomics on
tuberculosis drug discovery. Dntg Discov. Today, 11, 28-34.
Auerbach G, Herrmann A, Bracher A, Bader G. Gutlich M, Fischer M. Neukamm M. Garrido-Franco M,
Richardson J, Nar H, Huber R. Bacher A. (2000) Zinc plays a key role in human and bacterial GTP
cyclohydrolase I. Proc. Nat/. Acad. Sci. USA 97, 13567-13572.
Bacher A, Baur R, Eggers K, Harders H, Otto MK. Schnepple H. (1980) Riboflavin synthase of Bacillus
subtilis. Purification and properties. J. Bioi. Chem. 255, 632-637.
Bacher A, Le Van Q, Floss HG. (1983) Biosynthesis of riboflavin: Incorporation of 13C- labelled precursor
in to the Xylene ring. J. Bioi. Chem. 258, 13431-13437.
Bacher A. (1991) Chemistry and Biochemistry of Flavins (Muller.F .. ed) Chemical Rubber Co., Boca Raton.
Bauer S, Kemler K, Bacher A, Huber R, Fischer M, Steinbacher S. (2003) Crystal structure of
Schizosaccharomyces pombe riboflavin kinase reveals a novel ATP and riboflavin-binding fold. J. Mol. Bioi.
326, 1463-73.
Beach R, Plaut GWE. (1970) Stereospecificity of the enzymic synthesis of the 0-xylene ring of riboflavin. J.
Am. Chem. Soc. 92,2913-2916.
Boon C, Dick T. (2002) Mycobacterium bovis BCG response regulator essential for hypoxic dormancy. J.
Bacteriol. 184, 6760-6767.
Bradford MM. (1976) A rapid and sensitive method for the quantitation of microgram quantitites of protein
utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254.
Brown GM, Williamson M. (1982) Adv. Enzymol. Relat. Areas Mol. Bioi. 53,345-381.
Bryan K, Stormer FC. (1976) Decreased riboflavin formation in mutants of Aerobacter (Enterobacter)
aerogenes deficient in the butanediol pathway. Biochim. Biophys. Acta 428, 257-259
BurgAW, Brown GM. (1968) The biosynthesis of folic acid VIII. Purification and properties of the enzyme
that catalyzes the production of formate from carbon atom 8 of guanosine triphophate . J. Bioi. Chem. 243,
2349-2358.
Burrows RB, Brown GM. (1978) Presence of a deaminase and a reductase of Escherichia coli involved in
biosynthesis of riboflavin. J. Bacterial. 136, 657-667.
91
Bibliography
Campos JM, Simonetti JP, Pone MV, Carvalho LA, Pereira AC, Garrido JR. (1996) Disseminated Bacillus
Calmette-Guerin infection in HJV-infected children: case report and review. Paediatr. AIDS HJV infect. 1,
429-432.
Cole ST, Brosch R, Parkhill J, Gamier T, Churcher C. Harris D. Gordon SV, Eiglmeier K, Gas S, Barry
CE 3rd, et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome
sequence. Nature 393, 537-544.
Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, Honore N, Gamier T, Churcher C,
Harris D, Mungall K, Basham D, Brown D, Chillingworth T, Connor R, Davies RM, Devlin K, Duthoy S,
Feltwell T, Fraser A, Hamlin N, Holroyd S, Hornsby T, Jagels K, Lacroix C, Maclean J, Moule S, Murphy L,
Oliver K, Quail MA, Rajandream MA, Rutherford KM, Rutter S, Seeger K, Simon S, Simmonds M, Skelton
J, Squares R, Squares S, Stevens K, Taylor K, Whitehead S, Woodward JR, Barrell BG. (2001) Massive
gene decay in the leprosy bacillus. Nature 409, I 007-10 II.
Collaborative Computational Project Number 4: The CCP4 suite: programs for protein crystallography.
(1994) Acta Cryst D 50:760-763
Dahl JL, Kraus CN, Boshoff HI, Doan B, Foley K, Avarbock D. Kaplan G, Mizrahi V, Rubin H, Barry CE
3rd. (2003) The role of Rel~11 b-mediated adaptation to stationary phase in long-term persistence of
Mycobacterium tuberculosis in mice. Proc. Nat/. Acad. Sci. USA I 00, 10026-10031.
Das S, Kumar P, Bhor V, Surolia A, Vijayan M. (2006) lnvariance and variability in bacterial PanK: a study
based on the crystal structure of Mycobacterium tuberculosis PanK. Acta Crystallogr. D. Bioi. Crysta/logr.
62, 628-638.
Delano WL. (2002) The PyMOL molecular graphics system. Palo Alto, CA: Delano
Eberhardt S, Richter G, Gimbel W, Werner T, Bacher A. (1996) Cloning, sequencing, mapping and
hyperexpression of the ribC gene coding for riboflavin synthase of Escherichia coli. Eur. J. Biochem. 242,
712-719.
Eberhardt S, Zingler N, Kemter K, Richter G, Cushman M, Bacher A. (2001) Domain structure of riboflavin
synthase. Eur. J. Biochem. 268, 4315-4323.
Echt S, Bauer S, Steinbacher S, Huber R, Bacher A, Fischer M. (2004) Potential anti-infective targets in
pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida
albicans. J. Mol. Bioi. 341, 1085-1096.
Efimov l, Kuusk V, Zhang X, Mcintire WS. ( 1998) Proposed steady state kinetic mechanism for
Corynebacterium ammoniagenes FAD synthetase produced by Escherichia coli. Biochemistry 37, 97169723.
Eisenreich W, Bacher A, Arigoni D, and Rohdich F. (2004) Biosynthesis of isoprenoids via the nonmevalonate pathway. Cell Mol. Life Sci. 61, 1401-1426.
Emsley P, Cowtan K. (2004) Coot: model-building tools for molecular graphics. Acta Cryst. D 60, 21262132.
Enarson DA. (2003) Tuberculosis as a global public health problem. In Mycobacteria and TB (Kaufmann S.
H. E, Hahn, H. eds), Karger, Basel2, 1-16.
Fischer M, Schott AK. Romisch W, Ramsperger A. Augustin M. Fidler A. Bacher A. Richter G. Huber R,
Eisenreich W. (2004) Evolution of vitamin B2 biosynthesis. A novel class of riboflavin synthase in Archaea.
J. Mol. Bioi. 343, 267-278.
92
Bibliography
Fleischmann RD, Alland D, Eisen JA, Carpenter L, White 0, Peterson J, DeBoy R, Dodson R, Gwinn M,
Haft D et. a/. (2002) Whole genome comparison of Mycobacterium tuberculosis clinical and laboratory
strains. J. Bacteriol. 184, 5479-5490.
Foor F, Brown GM. (1975) Purification and properties of guanosine triphosphate cyclohydrolase II from
Escherichia coli. J. Bioi. Chem. 250, 3545-3551.
Frago S, Martinez-Julvez M, Serrano A, Medina M. (2008) Structural analysis of FAD synthetase from
Corynebacterium ammoniagenes. BMC Microbiol. 23, 160-168.
Frago S, Vehizquez-Campoy A, Medina M. (2009) The puzzle of ligand binding to Corynebacterium
ammoniagenes FAD synthetase. J. Bioi. Chem. 284,6610-6619.
French GS, Wilson KS. (1978) On the treatment of negative intensity observations. Acta. Cryst. A34, 517.
Galluccio M, Brizio C, Torchetti EM, Ferranti P, Gianazza E, lndiveri C, Barile M. (2007) Over-expression
in Escherichia coli, purification and characterization of isoform 2 of human FAD synthetase. Protein Expr.
Purif. 52, 175-181.
Gerdes SY, Scholle MD, D'Souza M, Bernal A. Baev MY, Farrell M, Kumasov OV, Daugherty MD, Mseeh
F, Polanuyer BM, Campbell JW, Anantha S, Shatalin KY. Chowdhury SA, Fonstein MY, Osterman AL.
(2002) From genetic footprinting to antimicrobial drug targets: examples in cofactor biosynthetic pathways.
J. Bacteriol. 184, 4555-4572.
Gerhardt S, Schott AK, Kairies N, Cushman M, lllarionov B, Eisenreich W, Bacher A, Huber R, Steinbacher
S, Fischer M. (2002) Studies on the reaction mechanism of riboflavin synthase: X-ray crystal structure of a
complex with 6-carboxyethyl-7-oxo-8-ribityllumazine. Stmcture 10, 13 71-1381.
Gladys FM, Plaut GWE. (1959) The isolation, synthesis and metabolic properties of 6, 7-Dimethyl-8ribityllumazine. J. Bioi. Chem. 234,641-647.
Harvey RA, Plaut GWE. (1966) Riboflavin synthase from yeast: Properties of complexes of the enzyme
with lumazine derivative and riboflavin. J. Bioi. Chem. 241, 2120-2136.
Hayden FG, Treanor JJ, Betts RF, Lobo M, Esinhart JD and Hussey EK. (1996) Safety and efficacy of the
neuraminidase inhibitor GG 167 in experimental human influenza. J. Americ. Medic. Associat. 275, 295-299.
Herguedas B, Martinez-Julvez M, Frago S, Medina M, Hermoso JA. (2010) Oligomeric state in the crystal
structure of modular FAD synthetase provides insights into its sequential catalysis in prokaryotes. J. Mol.
Bioi. 400, 218-230.
Her£ S, Eberhardt S, Bacher A. (2000) Biosynthesis of ribofavin in plants. The ribA gene of Arabidopsis
thaliana specifies a bifunctional GTP cyclohydrolase 11/3,4-dihydroxy-2-butanone 4-phosphate synthase.
Phytochemistry 53, 723-731.
Hollander IJ, Braman JC, Brown GM. (1980) Biosynthesis of riboflavin: Enzymatic conversion of 5-amino2,4-dioxy-6-ribitylaminopyrimidine to 6,7-dimethyl-8-ribityllumazine. Biochem. Biophys. Res. Commun. 94,
515-521.
Houben E, Nguyen L, Pieters J (2006). Interaction of pathogenic mycobacteria with the host immune system.
Curr. Opin. Microbial. 9, 7b--85.
Huerta C, Borek D, Machius M, Grishin NV, Zhang H. (2009) Structure and mechanism of a eukaryotic
FMN adenylyltransferase. J. Mol. Bioi. 389, 388-400.
93
Bibliography
Humbelin M, Van Loon APGM. (1999) GTP Cyclohydrolase II and 3,4-dihydroxy-2-butanone 4-phophate
synthase are rate limiting enzymes in riboflavin synthesis of an industrial Bacillus subtilis strain used for
riboflavin production . J. lnd Microbial. Biotechnol. 22, 1-7.
Huovinen P, Sundstrom L, Swedberg, G and Skold 0. (1995) Trimethoprim and sulfonamide resistance.
Antimicrob. Agents Chemother. 39, 279-289.
lllarionov B, Eisenreich W, Bacher A. (2001) A pentacyclic reaction intermediate of riboflavin synthase.
Proc. Nat/. Acad. Sci. USA 98, 7224-7229.
lllarionov B, Eisenreich W, Schramek N, Bacher A, Fischer M. (2005) Biosynthesis of vitamin B2:
diastereomeric reaction intermediates of archaeal and non-archaeal riboflavin synthases. J Bioi Chem. 280,
28541-28546.
lllarionov B, Haase I, Fischer M, Bacher A, Schramek N. (2005) Pre-steady-state kinetic analysis of
riboflavin synthase using a pentacyclic reaction intermediate as substrate. J. Bioi. Chem. 280, 28541-28546.
lllarionov B, Kemler K, Eberhardt S, Richter G, Cushman M, Bacher A. (2001) Riboflavin synthase of
Escherichia coli. Effect of single amino acid substitutions on reaction rate and ligand binding properties. J.
Bioi. Chem. 276, 11524-11530.
Johansen SK, Maus CE, Plikaytis BB and Douthwaite S. (2006) Capreomycin binds across the ribosomal
subunit interface using tlyA-encoded 2'-0-methylations in 16S and 23S rRNAs. Mol. Cell.. 23, 173-182.
Joms MS, Wang B, Jordan SP. (1987) Biochemistry 26,6810-6816.
Kabsch W. (1993) Automatic processing of rotation diffraction data from crystals of initially unknown
symmetry and cell constants. J. Appl. Cryst. 26, 795-800.
Kaiser J, Schrarnek N, Eberhardt S, Puttmer S, Schuster M and Bacher A. (2002) Biosynthesis of vitamin B2
An essential zinc ion at the catalytic site ofGTP cyclohydrolase II. Eur. J. Biochem. 269, 5264-5270.
Kaldor SW, Kalish VJ, Davies JF 2"d, Shetty BV, Fritz JE, Appelt K, Burgess JA, Campanale KM,
Chirgadze NY, Clawson OK. et. a/. (1997) Viracept (Nelfinavir Mesylate, AGI343): A potent, orally
bioavailable inhibitor of HIV-I protease. J. Med Chem. 40, 3979-3985.
Karthikeyan S, Zhou Q, Mseeh F, Grishin NV, Osterman AL, Zhang H. (2003) Crystal structure of human
riboflavin kinase reveals a beta barrel fold and a novel active site arch. Stntclllre 11, 265-273.
Kearney EB, Goldenberg J, Lipsick J, Perl M. (1979) Flavokinase and FAD synthetase from Bacillus subtilis
specific for reduced flavins. J. Bioi. Chem. 254, 9551-9557.
Kempf OJ, Norbeck OW, Codacovi L, Wang XC, Kohlbrenner WE, Wideburg NE, Paul DA, Knigge MF,
Vasavanonda S, Craig-Kennard A. et. a/. (1990) Structure-based, C2 symmetric inhibitors of HIV protease.
J. Medicinal Chem. 33, 2687-2689.
Kim CU, Lew W, Williams MA, Wu H, Zhang L, Swaminathan S, Bischofberger N, Chen MS, Mendel DB,
Laver WG, Stevens RC. (1997) Influenza neuraminidase inhibitors possessing a novel hydrophobic
interaction in the enzyme active site: Design, synthesis, and structural analysis of carbocyclic sialic acid
analogues with potent anti-influenza activity. J. Am. Chem. Soc. 119,681-690.
Kis K, Volk R, Bacher A. (1995) Biosynthesis of riboflavin. Studies on the reaction mechanism of 6,7dimethyl-8-ribityllumazine synthase. Biochemistry 34, 2883-2892.
Klebe G. (2000) Recent developments in structure-based drug design. J. Mol. Medicine. 18, 269-281.
94
Bibliography
Kubinyi H. (1999) Chance favours the prepared mind--from serendipity to rational drug design. J. Recept.
Signal Transduct. Res., 19, 15-39.
Kuhn P, Wilson K, Patch MG and Stevens RC. (2002) The genesis of high-throughput structure-based drug
discovery using protein crystallography. Curr. Opin. Chem. Bioi. 6, 704-710.
Kumar P, Singh M, Gautam R. Karthikeyan S. (20 10) Potential anti-bacterial drug target: Structural
characterization of 3,4-dihydroxy-2-butanone-4-phosphate synthase from Salmonella l)phimurium LT2.
Proteins: Struct .. Funct., Bioinf I 20806221 [Epub ahead of print].
Kuwada S, Masuda T, Kishi T, Asai M. (1958) Application of chromatography. XXXVI. Biosynthesis of
riboflavin. Riboflavin synthesizing enzyme extracted from Eremothecium ashbyi. Chem. Pharm. Bull.
(Tokyo) 6, 618-624.
Laemmli UK. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4.
Nature 227,680-685.
Lakowski RA. (2001) PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res. 29, 221-222.
Laskowski RA, MacArthur MW, Moss DS, Thornton JM. (1993) Procheck-a program to check the
stereochemical quality of protein structures. J. App. Crystallogr. 26. 283-291.
Lee JH. (1948) Tuberculosis and silicosis. Can. Med. Assoc. J. 58, 349-353.
Lee S, Ahn C, Park E, Hwang OS, Yim J. (2001) Biochemical characterization of ologomerization of
Escherichia coli GTP cyclohydrolase I. J. Biochem. Mol. Biol.35, 255-261.
Lehmann M, Degen S, Hohmann HP, Wyss M, Bacher A. Schramek N. (2009) Biosynthesis of riboflavin.
Screening for an improved GTP cyclohydrolase II mutant. FEBS J. 276, 4119-4129.
Leulliot N, Blondeau K, Keller J, Ulryck N, Quevillon-Cheruel S, van Tilbeurgh H. (2010) Crystal structure
of yeast FAD synthetase (Fad I) in complex with FAD. J. Mol. Bioi. 398,641-646.
Levine C, Hiasa H, Marians KJ. (1998) DNA gyrase and topoisomerase IV: biochemical activities,
physiological roles during chromosome replication, and drug sensitivities. Biochim. Biophys. Acta. 1400, 2943.
Li R, Sirawarapom R, Chitnumsub P, Sirawarapom W, Wooden J. Athappilly F, Turley S, Hoi WG. (2000)
Three-dimensional structure of Mycobacterium tuberculosis dihydrofolate reductase reveals opportunities for
the design of novel tuberculosis drugs. J. Mol. Bioi. 295, 307-323.
Liao 01, Calabrese JC, Wawrak Z, Viitanen PV, Jordan DB. (2001) Crystal structure of 3,4-<lihydroxy-2butanone 4-phosphate synthase of riboflavin biosynthesis. Structure 10. 11-18.
Liao 01, Wawrak Z, Calabrese JC. Viitanen PV, Jordan DB. (2001) Crystal structure of riboflavin synthase.
Structure 9, 399-408
Liao 01, Zheng YJ, Viitanen PV, Jordan DB. (2002) Structural definition of the active site and catalytic
mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase. Biochemistry 41, 1795-1806.
Lipton, SA and Bossy-Wetzel EJ. (2002) Ce/1111, 147-150.
Mack M, van Loon AP, Hohmann HP. (1998) Regulation of riboflavin biosynthesis in Bacillus subti/is is
affected by the activity of the flavokinase/flavin adenine dinucleotide synthetase encoded by ribC. J
Bacteriol. 180, 950-955.
95
Bibliography
Manstein OJ, Pai EF. (1986) Purification and characterization of FAD synthetase from Brevibacteriurn
arnrnoniagenes. J Bioi Chern. 261, 16169-16173.
Mashhadi Z, Zhang H. Xu H, White RH. (2008) Identification and characterization of an archaeon-specific
riboflavin kinase. J. Bacteriol. 190, 2615-2618.
Masuda T, Kiahi T, Asia M, Kuawada S. (1959) Application of chromatography. XXXVII. Total synthesis
of6,7-Dimethylribolumazine. Chern. Pharm. Bull. (Tokyo) 7, 361-365.
Masuda T. (1956) Application of chromatography. XXIX. G compound isolated from the Mycelium of
Erernothecium ashbyii. Chern. Pharrn. Bull. (Tokyo) 4, 375-381.
Masuda T. (1956) Isolation of green fluorescent substance produced by Eremothecium ashbyi . Chern.
Pharm. Bull. (To/..yo) 4, 71-72.
Masuda T. (1957) Application of chromatography. XXXI. Structure of green fluorescent substance produced
by Eremothecium ashbyii. Chern. Pharm. Bull. (Tokyo) 5, 28-30.
McCarthy AA, Peterson NA, Knijff Rand Baker EN. (2004) Crystal structure of MshB from Mycobacterium
hlberculosis, a deacetylase involved in mycothiol biosynthesis. J. Mol. Bioi. 335, 1131-II41.
McCoy AJ, Grosse-Kunstleve RW, Adams PD. Winn MD, Storoni LC, Read RJ. (2007) Phaser
crystallographic software. J. Appl. Cryst. 40, 658-674.
Meganathan R. (2001) Biosynthesis of menaquinone (vitamin K2) and ubiquinone (coenzyme Q): a
perspective on enzymatic mechanisms. Vitam. Horm. 61, 173-218.
Meining W, Eberhardt S, Bacher A, Ladenstein R. (2003) The structure of the N-terminal domain of
riboflavin synthase in complex with riboflavin at 2.6A resolution. J Mol Bioi. 331, I053-1063.
Meining W, Mort) S, Fischer M, Cushman M, Bacher A, Ladenstein R. (2000) The atomic structure of
pentameric lumazine synthase from Saccharomyces cerevisiae at 1.85 A resolution reveals the binding mode
of a phosphonate intermediate analogue. J. Mol. Bioi. 299, 181-197.
Meining W, Tibbelin G, Ladenstein R, Eberhardt S, Fisher M, Bacher A. (1998) Evidence for local 32
symmetry in homotrimeric riboflavin synthase of Escherichia coli. J. Stmct. Bioi. 121, 53-60.
Merrill AH, McCormick DB. (1980) Affinity chromatographic purification and properties of flavokinase
(A TP:ribiflavin 50-phosphotransferase) from rat liver. J. Bioi. Chern. 255, 1335-1338.
Morgunova E, Meining W, Illarionov B. Haase I, Jin G. Bacher A, Cushman M, Fischer M, Ladenstein R.
(2005) Crystal structure of lumazine synthase from Mycobacterium tuberculosis as a target for rational drug
design: binding mode of a new class of purinetrione inhibitors. Biochemistry 44, 2746-2758.
Munoz-Eiias EJ, McKinney JD. (2005) Mycobacterium tuberculosis isocitrate lyase I and are jointly
required for in vivo growth and virulence. Nat. Med. 11, 638-644.
Nar H. Huber R, Auerbach G, Fisher M. Hosl C. Ritz H. Racher A. Meining W, Eberhardt S, Bacher A.
(1995) Active site topology and reaction mechanism of GTP cyclohydrolase I. Proc. Nat/. Acad. Sci. USA
92, 12120-12125.
Nar H, Huber R, Meining W, Schmid C, Weinkauf S, Bacher A. (1995) Atomic structure of GTP
Cycloydrolase I. Stmcture 3, 459-466.
96
Bibliography
Neuberger G, Bacher A. (1986) Biosynthesis of riboflavin. Enzymatic formation of 6,7-dimethyl-8ribityllumazine by heavy riboflavin synthase from Bacillus subtilis. Biochem. Biophys. Res. Commun. 139,
llll-1116.
Nichol CA, Smith GK and Dutch OS. ( 1985) Biosynthesis and metabolism of tetrahydrobiopterin and
molybdopterin. Annu. Rev. Biochem. 54, 729-764.
Niculescu-Duvaz, I. (2001) Thymitaq (Zarix). Curr. Opin. lnvestig. Dmgs 2 , 693-705.
Niemann S, Rusch-Gerdes, S. (2003) Mycobacterium and TB - Therapy and drug resistance. In.
Mycobacteria and TB (Kaufmann S. H. E, Hahn, H. (eds.)), Karger, Basel 2, 84-96.
Oka M, McCormick DB. (1987) Complete purification and general characterization ofF AD synthetase from
rat liver. J Bioi Chem. 262, 7418-7422.
Otwinowski Z, Minor W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Meth.
Enzymol. 276, 307-326, C.W. Carter, Jr. & R.M. Sweet, Eds., Academic Press (New York).
Parish T, Stoker NG. (2002) The common aromatic amino acid biosynthesis pathway is essential in
Mycobacterium tuberculosis. Microbiology 148, 3069-3077.
Parrish NM, Dick JD and Bishai WR. (1998) Mechanism of latency in Mycobacterium tuberculosis. Tren.
Micro. 6, 107-112.
Pfyffer GE. (2003) Laboratory diagnosis of tuberculosis. ln. Mycobacteria and TB (Kaufmann S. H. E,
Hahn, H. eds), Karger, Basel2, 67-83.
Picollelli MA, Viitanen PV, Jordan DB. (2000) Spectrophotometric determination of 3,4-dihydroxy-2butanone-4-phosphate synthase activity. Anal. Biochem. 287, 347-349.
Plaut GWE, Broberg PL. (1956) Biosynthesis of riboflavin Ill. Incorporation of C
the ribityl side chain. J. Bioi. Chem. 219, 131-138.
14
labeled compounds in to
Plaut GWE. (1954) Biosynthesis of riboflavin: incorporation ofC 14 labeled compounds in to ring A. J. Bioi.
Chem. 211, 111-116.
Plaut GWE. (1960) Studies on the stoichometry of the enzymatic conversion of 6,7 dimethyl-8ribityllumazine to riboflavin. J. Bioi. Chem. 235, 41-42.
Plaut GWE. (1963) Studies on the nature of enzymic conversion of 6,7-dimethyl-8-ribityllumazine to
riboflavin. J. Bioi. Chem. 238, 2225.
Powers, H.J. (2003) Riboflavin (vitamin B-2) and health. Am. J. Clin. Nutr. 77, 1352-1360.
Ramachandran GN, Ramakrishnan C. Sasisekharan V (1963). Stereochemistry of polypeptide chain
configurations. J. Mol. Bioi. 7, 95-9.
Ramsperger A, Augustin M, Schott AK, Gerhardt S, Krojer T, Eisenreich W, Illarionov B, Cushman M,
Bacher A, Huber R, Fischer M. (2006) Crystal structure of an archaeal pentameric riboflavin synthase in
complex with a substrate analog inhibitor: stereochemical implications. J. Bioi. Chem. 281, 1224-1232
Rawat R, Whitty A, Tonge PJ. (2003) The isoniazid-NAD adduct is a slow, tight-binding inhibitor of lnhA,
the Mycobacterium tuberculosis enoyl reductase: adduct affinity and drug resistance. Proc. Nat/. Acad. Sci.
USA 100, 13881-13886.
97
Bibliography
Reichman LB. (2001) The world is different now. Timebomb: the global epidemic of multi-drug resistant
tuberculosis (Reichman, L. B. and Tanne, J. H., eds) MacGraw Hill, 23-41.
Ren J, Kotaka M, Lockyer M, Lamb HK, Hawkins AR, Stammers OK. (2005) GTP cyclohydrolase II
structure and mechanism. J. Bioi. Chem. 280, 36912-36919.
Richter G, Bacher A. (1997) Biosynthesis of riboflavin: 3,4-dihydroxy-2-butanone-4-phophate synthase.
Methods Enzymol. 280, 374-382.
Richter G, Fischer M, Krieger C, Eberhardt S, Liittgen H, Gerstenschlager I, BacherA. (1997) Biosynthesis
of riboflavin. Characterization of the bifunctional deaminase/reductase of Escherichia coli and Bacillus
subtilis. J Bacterial. 179 2022-2028.
Richter G, Ritz H, Katzenmeier G, Volk R, Kohnle A, Lottspeich F, Allendorf 0, Bacher A. (1993)
Biosynthesis of riboflavin: cloning, sequencing, mapping, and expression of the gene coding for GTP
cyclohydrolase II in Escherichia coli. J. Bacterial. 175, 4045-4051
Richter G, Volk R, Kreiger C, LahmHW, Roethlisberger U, Bacher A. (1992) Biosynthesis of riboflavin:
Cloning, sequencing, and expression of the gene coding for 3,4-dihydroxy-2-butanone 4-Phosphate synthase
of Escherichia coli. J. Bacterial. 174, 4050-4056.
Ritz H, Schramek N, Bracher A, Herz S, Eisenreich W, Richter G, Bacher A. (2001) Biosynthesis of
riboflavin. Studies on the mechanism ofGTP cyclohydrolase II. J. Bioi. Chem. 276,22273-22277.
Rodriguez GM, Voskuil Ml, Gold B, Schoolnik GK, Smith I. (2002) ideR, an essential gene m
Mycobacterium tuberculosis: role of ldeR in iron-dependent gene expression, iron metabolism, and oxidative
stress response. Infect. Jmmun. 70, 33 71-3381.
Ruiz P, Rodriguez-Cano F, Zerolo FJ, Casal M. (2002) Investigation of the in vitro activity of streptomycin
against Mycobacterium tuberculosis. Microb. Dntg Resist. 8, 147-149.
Sali A, Blundell TL. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Bioi.
234, 779-815.
Sambandamurthy VK, Wang X, Chen B, Russell RG, Derrick S, Collins FM, Morris SL, Jacobs WR Jr.
(2002) A pantothenate auxotroph of Mycobacterium tllberClllosis is highly attenuated and protects mice
against tuberculosis. Nat. Med. 8, 117 I-1174.
Sambrook J, and Russell OW. (2001) MoleCIIIar Cloning: A Laboratory Manual. (3rd edition). Cold Spring
Harbor Laboratory Press, USA.
Sandoval FJ and Roje S. (2005) An FMN hydrolase is fused to a riboflavin kinase homolog in plants. J. Bioi.
Chem. 280, 38337-38345.
Sandoval FJ, Zhang Y, Roje S. (2008) Flavin nucleotide metabolism in plants: monofunctional enzymes
synthesize fad in plastids. J. Bioi. Chem. 283, 30890-30900.
Santos MA, Jimenez A, Revue Ita JL. (2000) Molecular characterization of FMN I, the structural gene for the
monofunctional flavokinase of Saccharomyces cerevisiae. J. Bioi. Chem. 275,28618-28624.
Sareen 0, Newton GL, Fahey RC, Buchmeier NA. (2003) Mycothiol is essential for growth of
Mycobacterium tuberculosis Erdman. J. Bacterial. 185, 6736-6740.
Sassetti CM, Boyd DH, Rubin EJ. (2003) Genes required for mycobacterial growth defined by high density
mutagenesis. Mol. Microbial. 48, 77-84.
98
Bibliography
Scatena R. (2000). Prinomastat, a hydroxamate-based matrix metalloproteinase inhibitor. A novel
phannacological approach for tissue remodelling-related diseases. Expert Opin. lnvestig. Dmgs., 9, 21592165.
Schindler T, Bornmann W. Pellicena P, Miller WT, Clarkson B. Kuriyan J. (2000) Structural mechanism for
STI-571 inhibition of abelson tyrosine kinase. Science 289, 1938-1942.
Schott K. Kellennann J, Lottspeich F. Bacher A. (1 990) Riboflavin synthase of Bacillus subtilis.
Purification and amino acid sequence of the a subunit. J. Bioi. Chern. 265,4204-4209.
Shavlovsky GM, Logvinenko EM, Sibirnyi AA, Fedorovich DV, Zakalasky AE. (1981) Microbiology (Engl.
Transl. Mikrobiologiya) 50, 752-755.
Shrecker AW, Kornberg A. (1950) Reversible enzymatic synthesis of flavin-adenine dinuceotide. J. Bioi.
Chern. 145, 795-799.
Sobhanaditya J, Rao NA. (1 981) Plant flavokinase. Affinity-chromatographic procedure for the purification
of the enzyme from mung-bean (Phaseolus aureus) seeds and conformational changes on its interaction with
orthophosphate. Biochem. J. 197,227-232.
Solovieva IM, Kreneva RA, Leak OJ, Perumov DA. (1999) The ribR gene encodes a monofunctional
riboflavin kinase which is involved in regulation of the Bacillus subtilis riboflavin operon. Microbiology
145,67-73.
Steinbacher S, Schiffinann S, Richter G, Huber R, Bacher A, Fischer M. (2003) Structure of 3,4-dihydroxy2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and
the substrate ribulose 5-phosphate: implications for the catalytic mechanism. J. Bioi. Chern. 278, 4225642265.
Takayama K, Kilburn JO. (1 989) Inhibition of synthesis of arabinogalactan by ethambutol in Mycobacterium
smegmatis. Antimicrob. Agents Chemother. 33, 1493-1499.
Terwilliger TC, Park MS, Waldo GS, Berendzen J, Hung LW, Kim CY, Smith CV, Sacchettini JC,
Bellinzoni M, Bossi R, De Rossi E, Mattevi A, et. al. (2003). The TB structural genomics consortium: A
resource for TB biology. Tuberculosis, 83, 223-249.
Thompson JD, Higgins DG, Gibson TJ. (1994) CLUSTAL W: improving the sensitivity of progressive
multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix
choice. Nucleic Acids Res. 22, 4673-4680.
Thompson WJ, Fitzgerald PM, Holloway MK, Emini EA, Darke PL, McKeever BM, SchleifWA, Quintero J
C, Zugay JA, Tucker TJ, et. al. (1 992) Synthesis and antiviral activity of a series of HIV -I protease inhibitors
with functionality tethered to the P 1 or PI' phenyl substituents: X-ray crystal structure assisted design. J.
Med. Chen1. 35, I 685-170 I.
Timmins GS, Deretic V. (2006) Mechanisms of action of isoniazid. Mol. Microbial. 62, 1220-1227.
Vandal OH, Nathan CF, Ehrt S. (2009) Acid resistance in Mycobacterium tuberculosis. J. Bacterial. 191,
4714-4721.
Vetting MW, Roderick SL, Yu M, Blanchard JS. (2003) Crystal structure of mycothiol synthase (Rv0819)
from Mycobacterium tuberculosis shows structural homology to the GNAT family of N-acetyltransferases.
Protein Sci. 12, 1954-1959.
99
Bibliography
Yilcheze C, Weisbrod TR, Chen B, Kremer L, Hazbon MH. Wang F. Alland D, Sacchettini JC. Jacobs WR
Jr. (2005) Altered NADH/NAD+ ratio mediates coresistance to isoniazid and ethionamide in mycobacteria.
Antimicrob. Agents Chemother. 49, 708-720.
Yolk R, Bacher A. (1990) Studies on the 4-carbon precursor in the biosynthesis of riboflavin. Purification
and properties of L-3, 4-dihydroxy-2-butanone-4-phophate synthase. J. Bioi. Chem. 265, 19479-19485.
Yolk R, Bacher A. (1991) Biosynthesis of Riboflavin. Studies on the mechanism of L-3,4-dihydroxy-2butanone 4-phosphate synthase. J. Bioi. Chern. 266, 20610-20618.
Wang W, Kim R, Jancarik J, Yokota H. Kim SH. (2003) Crystal structure of a flavin-binding protein from
Thermotoga maritima. Proteins 52, 633-635.
Wang W, Kim R, Yokota H. Kim SH. (2005) Crystal structure of flavin binding to FAD synthetase of
Thermotoga maritima. Proteins 58, 246-248.
Wehrli W. (1983) Rifampin: mechanisms of action and resistance. Rev. Infect. Dis. 5, 407-411.
Williams SJ, Senaratne RH, Mougous JD, Riley LW and Bertozzi CR. (2002) 5' -adenosinephosphosulfate
lies at a metabolic branch point in mycobacteria. J. Bioi. Chern. 217,32606-32615.
Wise R, Andrews JM, Edwards LJ. (1983) In vitro activity of Bay 0986 7, a new quinoline derivative,
compared with those of other antimicrobial agents. Antimicrob. Agents Chemother. 23, 559-564.
World health organization (WHO): WHO report 2010
Wu M, Repetto B, Glerum OM, Tzagoloff A. (1995) Cloning and characterization of FADl, the structural
gene for flavin adenine dinucleotide synthetase of Saccharomyces cerevisiae. Mol. Cell. Bioi. IS, 264-271.
Yamada Y, Merrill AH, Jr, McCormick DB. ( 1990) Probable reaction mechanisms of flavokinase and FAD
synthetase from rat liver. Arch. Biochem. Biophys. 278, 125-130.
Zahrt TC, Deretic Y. (2000) An essential two-component signal transduction system in Mycobacterium
tuberculosis. J. Bacterial. 182, 3832-3838.
Zhang Y, Post-Martens K, Denkin S. (2006) New drug candidates and therapeutic targets for tuberculosis
therapy. Dntg Discov. Today ll, 21-27.
Zimhony 0, Cox JS, Welch JT, Yilcheze C. Jacobs WR, Jr. (2000) Pyrazinamide inhibits the eukaryotic-like
fatty acid synthase I (FASI) of Mycobacterium tubermlosis. Nat. Med. 6, I 043-1047.
100