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Mapping the ribonucleolytic active site of eosinophil-derived neurotoxin (EDN). High resolution crystal structures of EDN complexes with adenylic nucleotide inhibitors.

Leonidas DD, Boix E, Prill R, Suzuki M, Turton R, Minson K, Swaminathan GJ, Youle RJ, Acharya KR
J Biol Chem 276 15009-17 (2001)
Related entries: 1hi2, 1hi4, 1hi5

Cited: 27 times
EuropePMC logo PMID: 11154698

Abstract

Eosinophil-derived neurotoxin (EDN), a basic ribonuclease found in the large specific granules of eosinophils, belongs to the pancreatic RNase A family. Although its physiological function is still unclear, it has been shown that EDN is a neurotoxin capable of inducing the Gordon phenomenon in rabbits. EDN is also a potent helminthotoxin and can mediate antiviral activity of eosinophils against isolated virions of the respiratory syncytial virus. EDN is a catalytically efficient RNase sharing similar substrate specificity with pancreatic RNase A with its ribonucleolytic activity being absolutely essential for its neurotoxic, helminthotoxic, and antiviral activities. The crystal structure of recombinant human EDN in the unliganded form has been determined previously (Mosimann, S. C., Newton, D. L., Youle, R. J., and James, M. N. G. (1996) J. Mol. Biol. 260, 540-552). We have now determined high resolution (1.8 A) crystal structures for EDN in complex with adenosine-3',5'-diphosphate (3',5'-ADP), adenosine-2',5'-di-phosphate (2',5'-ADP), adenosine-5'-diphosphate (5'-ADP) as well as for a native structure in the presence of sulfate refined at 1.6 A. The inhibition constant of these mononucleotides for EDN has been determined. The structures present the first detailed picture of differences between EDN and RNase A in substrate recognition at the ribonucleolytic active site. They also provide a starting point for the design of tight-binding inhibitors, which may be used to restrain the RNase activity of EDN.

Articles - 1hi3 mentioned but not cited (3)

  1. High-resolution crystal structures of ribonuclease A complexed with adenylic and uridylic nucleotide inhibitors. Implications for structure-based design of ribonucleolytic inhibitors. Leonidas DD, Chavali GB, Oikonomakos NG, Chrysina ED, Kosmopoulou MN, Vlassi M, Frankling C, Acharya KR. Protein Sci. 12 2559-2574 (2003)
  2. Relating destabilizing regions to known functional sites in proteins. Dessailly BH, Lensink MF, Wodak SJ. BMC Bioinformatics 8 141 (2007)
  3. Eosinophils protect pressure overload- and β-adrenoreceptor agonist-induced cardiac hypertrophy. Yang C, Li J, Deng Z, Luo S, Liu J, Fang W, Liu F, Liu T, Zhang X, Zhang Y, Meng Z, Zhang S, Luo J, Liu C, Yang D, Liu L, Sukhova GK, Sadybekov A, Katritch V, Libby P, Wang J, Guo J, Shi GP. Cardiovasc Res 119 195-212 (2023)


Reviews citing this publication (4)

  1. Eosinophil granule proteins: form and function. Acharya KR, Ackerman SJ. J. Biol. Chem. 289 17406-17415 (2014)
  2. Mammalian antimicrobial proteins and peptides: overview on the RNase A superfamily members involved in innate host defence. Boix E, Nogués MV. Mol Biosyst 3 317-335 (2007)
  3. Structural determinants of the eosinophil cationic protein antimicrobial activity. Boix E, Salazar VA, Salazar VA, Torrent M, Pulido D, Nogués MV, Moussaoui M. Biol. Chem. 393 801-815 (2012)
  4. Nucleotide binding architecture for secreted cytotoxic endoribonucleases. Boix E, Blanco JA, Nogués MV, Moussaoui M. Biochimie 95 1087-1097 (2013)

Articles citing this publication (20)

  1. Eosinophil cationic protein (ECP) can bind heparin and other glycosaminoglycans through its RNase active site. Torrent M, Nogués MV, Boix E. J. Mol. Recognit. 24 90-100 (2011)
  2. Post-translational tyrosine nitration of eosinophil granule toxins mediated by eosinophil peroxidase. Ulrich M, Petre A, Youhnovski N, Prömm F, Schirle M, Schumm M, Pero RS, Doyle A, Checkel J, Kita H, Thiyagarajan N, Acharya KR, Schmid-Grendelmeier P, Simon HU, Schwarz H, Tsutsui M, Shimokawa H, Bellon G, Lee JJ, Przybylski M, Döring G. J. Biol. Chem. 283 28629-28640 (2008)
  3. Molecular recognition of human eosinophil-derived neurotoxin (RNase 2) by placental ribonuclease inhibitor. Iyer S, Holloway DE, Kumar K, Shapiro R, Acharya KR. J. Mol. Biol. 347 637-655 (2005)
  4. A simple assay for the ribonuclease activity of ribonucleases in the presence of ethidium bromide. Tripathy DR, Dinda AK, Dasgupta S. Anal. Biochem. 437 126-129 (2013)
  5. Inhibition of mammalian ribonucleases by endogenous adenosine dinucleotides. Kumar K, Jenkins JL, Jardine AM, Shapiro R. Biochem. Biophys. Res. Commun. 300 81-86 (2003)
  6. Role of catalytic and non-catalytic subsite residues in ribonuclease activity of human eosinophil-derived neurotoxin. Sikriwal D, Seth D, Batra JK. Biol. Chem. 390 225-234 (2009)
  7. The first crystal structure of human RNase 6 reveals a novel substrate-binding and cleavage site arrangement. Prats-Ejarque G, Arranz-Trullén J, Blanco JA, Pulido D, Nogués MV, Moussaoui M, Boix E. Biochem. J. 473 1523-1536 (2016)
  8. Influence of naturally-occurring 5'-pyrophosphate-linked substituents on the binding of adenylic inhibitors to ribonuclease a: an X-ray crystallographic study. Holloway DE, Chavali GB, Leonidas DD, Baker MD, Acharya KR. Biopolymers 91 995-1008 (2009)
  9. Crystallographic and functional studies of a modified form of eosinophil-derived neurotoxin (EDN) with novel biological activities. Chang C, Newton DL, Rybak SM, Wlodawer A. J. Mol. Biol. 317 119-130 (2002)
  10. Dinucleosides with non-natural backbones: a new class of ribonuclease A and angiogenin inhibitors. Debnath J, Dasgupta S, Pathak T. Chemistry 18 1618-1627 (2012)
  11. Increased expression of interferon-inducible protein-10 during surgically induced peritoneal injury. Mrstik M, Kotseos K, Ma C, Chegini N. Wound Repair Regen 11 120-126 (2003)
  12. Human eosinophil-derived neurotoxin: involvement of a putative non-catalytic phosphate-binding subsite in its catalysis. Sikriwal D, Seth D, Dey P, Batra JK. Mol. Cell. Biochem. 303 175-181 (2007)
  13. Sequence-specific backbone resonance assignments and microsecond timescale molecular dynamics simulation of human eosinophil-derived neurotoxin. Gagné D, Narayanan C, Bafna K, Charest LA, Agarwal PK, Doucet N. Biomol NMR Assign 11 143-149 (2017)
  14. Letter The ammonium sulfate inhibition of human angiogenin. Chatzileontiadou DS, Tsirkone VG, Dossi K, Kassouni AG, Liggri PG, Kantsadi AL, Stravodimos GA, Balatsos NA, Skamnaki VT, Leonidas DD. FEBS Lett. 590 3005-3018 (2016)
  15. Functional characterization of ECP-heparin interaction: a novel molecular model. Hung TJ, Tomiya N, Chang TH, Cheng WC, Kuo PH, Ng SK, Lien PC, Lee YC, Chang MD. PLoS ONE 8 e82585 (2013)
  16. Structural basis of substrate specificity in porcine RNase 4. Liang S, Acharya KR. FEBS J. 283 912-928 (2016)
  17. Basic amino acid residues of human eosinophil derived neurotoxin essential for glycosaminoglycan binding. Hung TJ, Chang WT, Tomiya N, Lee YC, Chang HT, Chen CJ, Kuo PH, Fan TC, Chang MD. Int J Mol Sci 14 19067-19085 (2013)
  18. Carboxymethylsulfonylated Ribopyrimidines: Rational Design of Ribonuclease A Inhibitors Employing Chemical Logic. Datta D, Dasgupta S, Pathak T. ChemMedChem 11 620-628 (2016)
  19. Evolutionary Trends in RNA Base Selectivity Within the RNase A Superfamily. Prats-Ejarque G, Lu L, Salazar VA, Moussaoui M, Boix E. Front Pharmacol 10 1170 (2019)
  20. Sulfonic nucleic acids (SNAs): a new class of substrate mimics for ribonuclease A inhibition. Datta D, Dasgupta S, Pathak T. Org Biomol Chem 17 7215-7221 (2019)


Related citations provided by authors (1)

  1. X-ray crystallographic structure of recombinant eosinophil-derived neurotoxin at 1.83 A resolution.. Mosimann SC, Newton DL, Youle RJ, James MN J Mol Biol 260 540-52 (1996)

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