Domain organization in Candida glabrata THI6, a bifunctional enzyme required for thiamin biosynthesis in eukaryotes.

THI6 is a bifunctional enzyme found in the thiamin biosynthetic pathway in eukaryotes. The N-terminal domain of THI6 catalyzes the ligation of the thiamin thiazole and pyrimidine moieties to form thiamin phosphate, and the C-terminal domain catalyzes the phosphorylation of 4-methyl-5-hydroxyethylthiazole in a salvage pathway. In prokaryotes, thiamin phosphate synthase and 4-methyl-5-hydroxyethylthiazole kinase are separate gene products. Here we report the first crystal structure of a eukaryotic THI6 along with several complexes that characterize the active sites responsible for the two chemical reactions. THI6 from Candida glabrata is a homohexamer in which the six protomers form a cage-like structure. Each protomer is composed of two domains, which are structurally homologous to their monofunctional bacterial counterparts. Two loop regions not found in the bacterial enzymes provide interactions between the two domains. The structures of different protein-ligand complexes define the thiazole and ATP binding sites of the 4-methyl-5-hydroxyethylthiazole kinase domain and the thiazole phosphate and 4-amino-5-hydroxymethyl-2-methylpyrimidine pyrophosphate binding sites of the thiamin phosphate synthase domain. Our structural studies reveal that the active sites of the two domains are 40 Å apart and are not connected by an obvious channel. Biochemical studies show 4-methyl-5-hydroxyethylthiazole phosphate is a substrate for THI6; however, adenosine diphospho-5β-ethyl-4-methylthiazole-2-carboxylic acid, the product of THI4, is not a substrate for THI6. This suggests that an unidentified enzyme is necessary to produce the substrate for THI6 from the THI4 product.

[1]  T. Begley,et al.  The structural and biochemical foundations of thiamin biosynthesis. , 2009, Annual review of biochemistry.

[2]  A. Chatterjee,et al.  Biosynthesis of the thiamin thiazole in Bacillus subtilis: identification of the product of the thiazole synthase-catalyzed reaction. , 2009, Journal of the American Chemical Society.

[3]  C. Krebs,et al.  Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. , 2008, Nature chemical biology.

[4]  D. Downs,et al.  ThiC is an [Fe-S] cluster protein that requires AdoMet to generate the 4-amino-5-hydroxymethyl-2-methylpyrimidine moiety in thiamin synthesis. , 2008, Biochemistry.

[5]  C. Kinsland,et al.  Structural studies of thiamin monophosphate kinase in complex with substrates and products. , 2008, Biochemistry.

[6]  K. Henrick,et al.  Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.

[7]  T. Begley,et al.  Thiamin phosphate synthase: the rate of pyrimidine carbocation formation. , 2007, Journal of the American Chemical Society.

[8]  A. Chatterjee,et al.  Structural insights into the function of the thiamin biosynthetic enzyme Thi4 from Saccharomyces cerevisiae. , 2006, Biochemistry.

[9]  A. Chatterjee,et al.  Thiamin biosynthesis in eukaryotes: characterization of the enzyme-bound product of thiazole synthase from Saccharomyces cerevisiae and its implications in thiazole biosynthesis. , 2006, Journal of the American Chemical Society.

[10]  T. Begley,et al.  Thi20, a remarkable enzyme from Saccharomyces cerevisiae with dual thiamin biosynthetic and degradation activities. , 2005, Bioorganic chemistry.

[11]  T. Begley,et al.  Structural characterization of the regulatory proteins TenA and TenI from Bacillus subtilis and identification of TenA as a thiaminase II. , 2005, Biochemistry.

[12]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[13]  P. Dorrestein,et al.  The biosynthesis of the thiazole phosphate moiety of thiamin: the sulfur transfer mediated by the sulfur carrier protein ThiS. , 2004, Chemistry & biology.

[14]  R. Mehl,et al.  Biosynthesis of the thiamin pyrimidine: the reconstitution of a remarkable rearrangement reaction. , 2004, Organic & biomolecular chemistry.

[15]  R. Butterworth Thiamin deficiency and brain disorders , 2003, Nutrition Research Reviews.

[16]  J. Zeidler,et al.  Biosynthesis of vitamin B1 in yeast. Derivation of the pyrimidine unit from pyridoxine and histidine. Intermediacy of urocanic acid. , 2003, Journal of the American Chemical Society.

[17]  Frank Jordan,et al.  Current mechanistic understanding of thiamin diphosphate-dependent enzymatic reactions. , 2003, Natural product reports.

[18]  Peter Robert Martin,et al.  The Role of Thiamine Deficiency in Alcoholic Brain Disease , 2003, Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism.

[19]  M. Gelfand,et al.  Comparative Genomics of Thiamin Biosynthesis in Procaryotes , 2002, The Journal of Biological Chemistry.

[20]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination , 2022 .

[21]  Tadhg P Begley,et al.  Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate kinase from Salmonella typhimurium at 2.3 A resolution. , 2002, Structure.

[22]  W. Delano The PyMOL Molecular Graphics System , 2002 .

[23]  S E Ealick,et al.  Structural characterization of the enzyme-substrate, enzyme-intermediate, and enzyme-product complexes of thiamin phosphate synthase. , 2001, Biochemistry.

[24]  T. Begley,et al.  Mechanistic studies on thiamin phosphate synthase: evidence for a dissociative mechanism. , 2001, Biochemistry.

[25]  F. Raushel,et al.  Channeling of substrates and intermediates in enzyme-catalyzed reactions. , 2001, Annual review of biochemistry.

[26]  H. Chiu,et al.  Crystal structure of thiamin phosphate synthase from Bacillus subtilis at 1.25 A resolution. , 1999, Biochemistry.

[27]  Patrice Gouet,et al.  ESPript: analysis of multiple sequence alignments in PostScript , 1999, Bioinform..

[28]  S E Ealick,et al.  Structure of human adenosine kinase at 1.5 A resolution. , 1998, Biochemistry.

[29]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[30]  T A Jones,et al.  Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8 A resolution: insights into a new family of kinase structures. , 1998, Structure.

[31]  D. Downs,et al.  Characterization of thiL, Encoding Thiamin-monophosphate Kinase, in Salmonella typhimurium * , 1997, The Journal of Biological Chemistry.

[32]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[33]  G J Kleywegt,et al.  xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. , 1996, Acta crystallographica. Section D, Biological crystallography.

[34]  D. M. F. Aalten,et al.  PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules , 1996, J. Comput. Aided Mol. Des..

[35]  Y. Kawasaki,et al.  Isolation and characterization of the THI6 gene encoding a bifunctional thiamin-phosphate pyrophosphorylase/hydroxyethylthiazole kinase from Saccharomyces cerevisiae. , 1994, The Journal of biological chemistry.

[36]  Julie Dawn Thompson,et al.  Improved sensitivity of profile searches through the use of sequence weights and gap excision , 1994, Comput. Appl. Biosci..

[37]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.

[38]  Y. Kawasaki Copurification of hydroxyethylthiazole kinase and thiamine-phosphate pyrophosphorylase of Saccharomyces cerevisiae: characterization of hydroxyethylthiazole kinase as a bifunctional enzyme in the thiamine biosynthetic pathway , 1993, Journal of bacteriology.

[39]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[40]  E. Monsen The 10th edition of the Recommended Dietary Allowances: what's new in the 1989 RDAs? , 1989, Journal of the American Dietetic Association.

[41]  M. M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[42]  B. Matthews Solvent content of protein crystals. , 1968, Journal of molecular biology.