1g8f Citations

Crystal structure of ATP sulfurylase from Saccharomyces cerevisiae, a key enzyme in sulfate activation.

EMBO J 20 316-29 (2001)
Related entries: 1g8g, 1g8h

Cited: 51 times
EuropePMC logo PMID: 11157739

Abstract

ATP sulfurylases (ATPSs) are ubiquitous enzymes that catalyse the primary step of intracellular sulfate activation: the reaction of inorganic sulfate with ATP to form adenosine-5'-phosphosulfate (APS) and pyrophosphate (PPi). With the crystal structure of ATPS from the yeast Saccharomyces cerevisiae, we have solved the first structure of a member of the ATP sulfurylase family. We have analysed the crystal structure of the native enzyme at 1.95 Angstroms resolution using multiple isomorphous replacement (MIR) and, subsequently, the ternary enzyme product complex with APS and PPi bound to the active site. The enzyme consists of six identical subunits arranged in two stacked rings in a D:3 symmetric assembly. Nucleotide binding causes significant conformational changes, which lead to a rigid body structural displacement of domains III and IV of the ATPS monomer. Despite having similar folds and active site design, examination of the active site of ATPS and comparison with known structures of related nucleotidylyl transferases reveal a novel ATP binding mode that is peculiar to ATP sulfurylases.

Reviews - 1g8f mentioned but not cited (1)

Articles - 1g8f mentioned but not cited (6)

  1. Crystal structure of ATP sulfurylase from Saccharomyces cerevisiae, a key enzyme in sulfate activation. Ullrich TC, Blaesse M, Huber R. EMBO J 20 316-329 (2001)
  2. Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. Felts AK, Gallicchio E, Chekmarev D, Paris KA, Friesner RA, Levy RM. J Chem Theory Comput 4 855-868 (2008)
  3. Structural genomics reveals EVE as a new ASCH/PUA-related domain. Bertonati C, Punta M, Fischer M, Yachdav G, Forouhar F, Zhou W, Kuzin AP, Seetharaman J, Abashidze M, Ramelot TA, Kennedy MA, Cort JR, Belachew A, Hunt JF, Tong L, Montelione GT, Rost B. Proteins 75 760-773 (2009)
  4. Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major. Arakaki T, Le Trong I, Phizicky E, Quartley E, DeTitta G, Luft J, Lauricella A, Anderson L, Kalyuzhniy O, Worthey E, Myler PJ, Kim D, Baker D, Hol WG, Merritt EA. Acta Crystallogr Sect F Struct Biol Cryst Commun 62 175-179 (2006)
  5. The crystal structure of a novel SAM-dependent methyltransferase PH1915 from Pyrococcus horikoshii. Sun W, Xu X, Pavlova M, Edwards AM, Joachimiak A, Savchenko A, Christendat D. Protein Sci 14 3121-3128 (2005)
  6. Mechanism of Sulfate Activation Catalyzed by ATP Sulfurylase - Magnesium Inhibits the Activity. Wójcik-Augustyn A, Johansson AJ, Borowski T. Comput Struct Biotechnol J 17 770-784 (2019)


Reviews citing this publication (9)

  1. Sulfur assimilation and glutathione metabolism under cadmium stress in yeast, protists and plants. Mendoza-Cózatl D, Loza-Tavera H, Hernández-Navarro A, Moreno-Sánchez R. FEMS Microbiol Rev 29 653-671 (2005)
  2. The globally widespread genus Sulfurimonas: versatile energy metabolisms and adaptations to redox clines. Han Y, Perner M. Front Microbiol 6 989 (2015)
  3. Sulfate metabolism in mycobacteria. Schelle MW, Bertozzi CR. Chembiochem 7 1516-1524 (2006)
  4. Structural biology of plant sulfur metabolism: from assimilation to biosynthesis. Ravilious GE, Jez JM. Nat Prod Rep 29 1138-1152 (2012)
  5. Diversity and regulation of ATP sulfurylase in photosynthetic organisms. Prioretti L, Gontero B, Hell R, Giordano M. Front Plant Sci 5 597 (2014)
  6. Key bacterial multi-centered metal enzymes involved in nitrate and sulfate respiration. Fritz G, Einsle O, Rudolf M, Schiffer A, Kroneck PM. J Mol Microbiol Biotechnol 10 223-233 (2005)
  7. Structural biology and regulation of the plant sulfation pathway. Jez JM, Ravilious GE, Herrmann J. Chem Biol Interact 259 31-38 (2016)
  8. Conserving energy with sulfate around 100 °C--structure and mechanism of key metal enzymes in hyperthermophilic Archaeoglobus fulgidus. Parey K, Fritz G, Ermler U, Kroneck PM. Metallomics 5 302-317 (2013)
  9. Structural biology of plant sulfur metabolism: from sulfate to glutathione. Jez JM. J Exp Bot 70 4089-4103 (2019)

Articles citing this publication (35)

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  2. Convergent evolution of enzyme active sites is not a rare phenomenon. Gherardini PF, Wass MN, Helmer-Citterich M, Sternberg MJ. J Mol Biol 372 817-845 (2007)
  3. Structure of human NMN adenylyltransferase. A key nuclear enzyme for NAD homeostasis. Garavaglia S, D'Angelo I, Emanuelli M, Carnevali F, Pierella F, Magni G, Rizzi M. J Biol Chem 277 8524-8530 (2002)
  4. Crystal structures of E. coli nicotinate mononucleotide adenylyltransferase and its complex with deamido-NAD. Zhang H, Zhou T, Kurnasov O, Cheek S, Grishin NV, Osterman A. Structure 10 69-79 (2002)
  5. Molecular basis for G protein control of the prokaryotic ATP sulfurylase. Mougous JD, Lee DH, Hubbard SC, Schelle MW, Vocadlo DJ, Berger JM, Bertozzi CR. Mol Cell 21 109-122 (2006)
  6. Identification and characterization of salt-responsive microRNAs in Populus tomentosa by high-throughput sequencing. Ren Y, Chen L, Zhang Y, Kang X, Zhang Z, Wang Y. Biochimie 95 743-750 (2013)
  7. The crystal structure of human PAPS synthetase 1 reveals asymmetry in substrate binding. Harjes S, Bayer P, Scheidig AJ. J Mol Biol 347 623-635 (2005)
  8. Soybean ATP sulfurylase, a homodimeric enzyme involved in sulfur assimilation, is abundantly expressed in roots and induced by cold treatment. Phartiyal P, Kim WS, Cahoon RE, Jez JM, Krishnan HB. Arch Biochem Biophys 450 20-29 (2006)
  9. Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis. Taniguchi T, Miyauchi K, Sakaguchi Y, Yamashita S, Soma A, Tomita K, Suzuki T. Nat Chem Biol 14 1010-1020 (2018)
  10. Alteration of lithium pharmacology through manipulation of phosphoadenosine phosphate metabolism. Spiegelberg BD, Dela Cruz J, Law TH, York JD. J Biol Chem 280 5400-5405 (2005)
  11. Genome-wide analysis of salt-responsive and novel microRNAs in Populus euphratica by deep sequencing. Si J, Zhou T, Bo W, Xu F, Wu R. BMC Genet 15 Suppl 1 S6 (2014)
  12. Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate. Carlson HK, Kuehl JV, Hazra AB, Justice NB, Stoeva MK, Sczesnak A, Mullan MR, Iavarone AT, Engelbrektson A, Price MN, Deutschbauer AM, Arkin AP, Coates JD. ISME J 9 1295-1305 (2015)
  13. Structure and mechanism of soybean ATP sulfurylase and the committed step in plant sulfur assimilation. Herrmann J, Ravilious GE, McKinney SE, Westfall CS, Lee SG, Baraniecka P, Giovannetti M, Kopriva S, Krishnan HB, Jez JM. J Biol Chem 289 10919-10929 (2014)
  14. Crystal structure of human nicotinamide mononucleotide adenylyltransferase in complex with NMN. Werner E, Ziegler M, Lerner F, Schweiger M, Heinemann U. FEBS Lett 516 239-244 (2002)
  15. Crystal structure of the bifunctional ATP sulfurylase-APS kinase from the chemolithotrophic thermophile Aquifex aeolicus. Yu Z, Lansdon EB, Segel IH, Fisher AJ. J Mol Biol 365 732-743 (2007)
  16. The complex structures of ATP sulfurylase with thiosulfate, ADP and chlorate reveal new insights in inhibitory effects and the catalytic cycle. Ullrich TC, Huber R. J Mol Biol 313 1117-1125 (2001)
  17. Comparative Genomics and Proteomic Analysis of Assimilatory Sulfate Reduction Pathways in Anaerobic Methanotrophic Archaea. Yu H, Susanti D, McGlynn SE, Skennerton CT, Chourey K, Iyer R, Scheller S, Tavormina PL, Hettich RL, Mukhopadhyay B, Orphan VJ. Front Microbiol 9 2917 (2018)
  18. Structural, biochemical and genetic characterization of dissimilatory ATP sulfurylase from Allochromatium vinosum. Parey K, Demmer U, Warkentin E, Wynen A, Ermler U, Dahl C. PLoS One 8 e74707 (2013)
  19. Sulfate activation enzymes: phylogeny and association with pyrophosphatase. Bradley ME, Rest JS, Li WH, Schwartz NB. J Mol Evol 68 1-13 (2009)
  20. Time-specific and pleiotropic quantitative trait loci coordinately modulate stem growth in Populus. Du Q, Yang X, Xie J, Quan M, Xiao L, Lu W, Tian J, Gong C, Chen J, Li B, Zhang D. Plant Biotechnol J 17 608-624 (2019)
  21. ATP sulfurylase from the hyperthermophilic chemolithotroph Aquifex aeolicus. Hanna E, MacRae IJ, Medina DC, Fisher AJ, Segel IH. Arch Biochem Biophys 406 275-288 (2002)
  22. Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH. Christensen GA, Zane GM, Kazakov AE, Li X, Rodionov DA, Novichkov PS, Dubchak I, Arkin AP, Wall JD. J Bacteriol 197 29-39 (2015)
  23. Kinetic mechanism of the dimeric ATP sulfurylase from plants. Ravilious GE, Herrmann J, Goo Lee S, Westfall CS, Jez JM. Biosci Rep 33 e00053 (2013)
  24. Mononuclear versus dinuclear complex formation in nickel(II) sulfate/phenyl(2-pyridyl)ketone oxime chemistry depending on the ligand to metal reaction ratio: synthetic, spectral and structural studies. Papatriantafyllopoulou C, Efthymiou CG, Raptopoulou CP, Terzis A, Manessi-Zoupa E, Perlepes SP. Spectrochim Acta A Mol Biomol Spectrosc 70 718-728 (2008)
  25. A Model Roseobacter, Ruegeria pomeroyi DSS-3, Employs a Diffusible Killing Mechanism To Eliminate Competitors. Sharpe GC, Gifford SM, Septer AN. mSystems 5 e00443-20 (2020)
  26. Kinetic properties of ATP sulfurylase and APS kinase from Thiobacillus denitrificans. Gay SC, Fribourgh JL, Donohoue PD, Segel IH, Fisher AJ. Arch Biochem Biophys 489 110-117 (2009)
  27. Propionibacterium freudenreichii thrives in microaerobic conditions by complete oxidation of lactate to CO2. Dank A, van Mastrigt O, Boeren S, Lillevang SK, Abee T, Smid EJ. Environ Microbiol 23 3116-3129 (2021)
  28. Temperature effects on the allosteric transition of ATP sulfurylase from Penicillium chrysogenum. Medina DC, Hanna E, MacRae IJ, Fisher AJ, Segel IH. Arch Biochem Biophys 393 51-60 (2001)
  29. Use of the cysteine-repressible HpMET3 promoter as a novel tool to regulate gene expression in Hansenula polymorpha. Yoo SJ, Chung SY, Lee DJ, Kim H, Cheon SA, Kang HA. Biotechnol Lett 37 2237-2245 (2015)
  30. Cloning of the ATP sulphurylase gene of Schizosaccharomyces pombe by functional complementation. Simonics T, Maráz A. Can J Microbiol 54 71-74 (2008)
  31. FgMet3 and FgMet14 related to cysteine and methionine biosynthesis regulate vegetative growth, sexual reproduction, pathogenicity, and sensitivity to fungicides in Fusarium graminearum. Zhao F, Yuan Z, Wen W, Huang Z, Mao X, Zhou M, Hou Y. Front Plant Sci 13 1011709 (2022)
  32. Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria. Saxena P, Rauniyar S, Thakur P, Singh RN, Bomgni A, Alaba MO, Tripathi AK, Gnimpieba EZ, Lushbough C, Sani RK. Front Microbiol 14 1086021 (2023)
  33. Changes in ATP Sulfurylase Activity in Response to Altered Cyanobacteria Growth Conditions. Gastoldi L, Ward LM, Nakagawa M, Giordano M, McGlynn SE. Microbes Environ 36 (2021)
  34. Cloning, expression and bioinformatics analysis of ATP sulfurylase from Acidithiobacillus ferrooxidans ATCC 23270 in Escherichia coli. Jaramillo ML, Abanto M, Quispe RL, Calderón J, Del Valle LJ, Talledo M, Ramírez P. Bioinformation 8 695-704 (2012)
  35. Purification, crystallization and preliminary X-ray diffraction analysis of adenosine triphosphate sulfurylase (ATPS) from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774. Gavel OY, Kladova AV, Bursakov SA, Dias JM, Texeira S, Shnyrov VL, Moura JJ, Moura I, Romão MJ, Trincão J. Acta Crystallogr Sect F Struct Biol Cryst Commun 64 593-595 (2008)