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Crystal structures of Urtica dioica agglutinin and its complex with tri-N-acetylchitotriose.

Harata K, Muraki M
J Mol Biol 297 673-81 (2000)
Cited: 36 times
EuropePMC logo PMID: 10731420

Abstract

Urtica dioica agglutinin is a small plant lectin that binds chitin. We purified the isolectin VI (UDA-VI) and crystal structures of the isolectin and its complex with tri-N-acetylchitotriose (NAG3) were determined by X-ray analysis. The UDA-VI consists of two domains analogous to hevein and the backbone folding of each domain is maintained by four disulfide bridges. The sequence similarity of the two domains is not high (42 %) but their backbone structures are well superimposed except some loop regions. The chitin binding sites are located on the molecular surface at both ends of the dumbbell-shape molecule. The crystal of the NAG3 complex contains two independent molecules forming a protein-sugar 2:2 complex. One NAG3 molecule is sandwiched between two independent UDA-VI molecules and the other sugar molecule is also sandwiched by one UDA-VI molecule and symmetry-related another one. The sugar binding site of N-terminal domain consists of three subsites accommodating NAG3 while two NAG residues are bound to the C-terminal domain. In each sugar-binding site, three aromatic amino acid residues and one serine residue participate to the NAG3 binding. The sugar rings bound to two subsites are stacked to the side-chain groups of tryptophan or histidine and a tyrosine residue is in face-to-face contact with an acetylamino group, to which the hydroxyl group of a serine residue is hydrogen-bonded. The third subsite of the N-terminal domain binds a NAG moiety with hydrogen bonds. The results suggest that the triad of aromatic amino acid residues is intrinsic in sugar binding of hevein-like domains.

Reviews - 1ehh mentioned but not cited (1)

  1. Targeting the glycans of glycoproteins: a novel paradigm for antiviral therapy. Balzarini J. Nat. Rev. Microbiol. 5 583-597 (2007)

Articles - 1ehh mentioned but not cited (1)

  1. Structural investigation of a novel N-acetyl glucosamine binding chi-lectin which reveals evolutionary relationship with class III chitinases. Patil DN, Datta M, Dev A, Dhindwal S, Singh N, Dasauni P, Kundu S, Sharma AK, Tomar S, Kumar P. PLoS ONE 8 e63779 (2013)


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  1. Antimicrobial Peptides from Plants. Tam JP, Wang S, Wong KH, Tan WL. Pharmaceuticals (Basel) 8 711-757 (2015)
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  6. Therapeutic Potentials of Antiviral Plants Used in Traditional African Medicine With COVID-19 in Focus: A Nigerian Perspective. Attah AF, Fagbemi AA, Olubiyi O, Dada-Adegbola H, Oluwadotun A, Elujoba A, Babalola CP. Front Pharmacol 12 596855 (2021)
  7. Lectins and lectibodies: potential promising antiviral agents. Nabi-Afjadi M, Heydari M, Zalpoor H, Arman I, Sadoughi A, Sahami P, Aghazadeh S. Cell Mol Biol Lett 27 37 (2022)

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  13. Glycan structures and antiviral effect of the structural subunit RvH2 of Rapana hemocyanin. Dolashka P, Velkova L, Shishkov S, Kostova K, Dolashki A, Dimitrov I, Atanasov B, Devreese B, Voelter W, Van Beeumen J. Carbohydr. Res. 345 2361-2367 (2010)
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  15. Mutational analysis of the binding affinity and transport activity for N-acetylglucosamine of the novel ABC transporter Ngc in the chitin-degrader Streptomyces olivaceoviridis. Saito A, Schrempf H. Mol. Genet. Genomics 271 545-553 (2004)
  16. The tomato lectin consists of two homologous chitin-binding modules separated by an extensin-like linker. Peumans WJ, Rougé P, Van Damme EJ. Biochem. J. 376 717-724 (2003)
  17. Similarity between protein-protein and protein-carbohydrate interactions, revealed by two crystal structures of lectins from the roots of pokeweed. Hayashida M, Fujii T, Hamasu M, Ishiguro M, Hata Y. J. Mol. Biol. 334 551-565 (2003)
  18. The chitin-binding capability of Cy-AMP1 from cycad is essential to antifungal activity. Yokoyama S, Iida Y, Kawasaki Y, Minami Y, Watanabe K, Yagi F. J. Pept. Sci. 15 492-497 (2009)
  19. Folding and homodimerization of wheat germ agglutinin. Portillo-Téllez Mdel C, Bello M, Salcedo G, Gutiérrez G, Gómez-Vidales V, García-Hernández E. Biophys. J. 101 1423-1431 (2011)
  20. Insights into the dynamics and molecular recognition features of glycopeptides by protein receptors: the 3D solution structure of hevein bound to the trisaccharide core of N-glycoproteins. Hernández-Gay JJ, Ardá A, Eller S, Mezzato S, Leeflang BR, Unverzagt C, Cañada FJ, Jiménez-Barbero J. Chemistry 16 10715-10726 (2010)
  21. Large-molecular-weight carbohydrate-binding agents as HIV entry inhibitors targeting glycoprotein gp120. Balzarini J. Curr Opin HIV AIDS 1 355-360 (2006)
  22. Sugar-Binding Profiles of Chitin-Binding Lectins from the Hevein Family: A Comprehensive Study. Itakura Y, Nakamura-Tsuruta S, Kominami J, Tateno H, Hirabayashi J. Int J Mol Sci 18 (2017)
  23. Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies. Lokhande KB, Apte GR, Shrivastava A, Singh A, Pal JK, K Venkateswara Swamy, Gupta RK. J Biomol Struct Dyn 40 3880-3898 (2022)
  24. Molecular structure and properties of lectin from tomato fruit. Oguri S, Amano K, Nakashita H, Nagata Y, Momonoki YS. Biosci. Biotechnol. Biochem. 72 2640-2650 (2008)
  25. In Vitro Characterization of the Carbohydrate-Binding Agents HHA, GNA, and UDA as Inhibitors of Influenza A and B Virus Replication. Vanderlinden E, Van Winkel N, Naesens L, Van Damme EJM, Persoons L, Schols D. Antimicrob Agents Chemother 65 e01732-20 (2021)
  26. Isolation and characterization of isolectins from Talisia esculenta seeds. Freire MG, Machado OL, Smolka MB, Marangoni S, Novello JC, Macedo ML. J Protein Chem 20 495-500 (2001)
  27. Datura stramonium agglutinin: cloning, molecular characterization and recombinant production in Arabidopsis thaliana. Nishimoto K, Tanaka K, Murakami T, Nakashita H, Sakamoto H, Oguri S. Glycobiology 25 157-169 (2015)


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