Structural analysis of Ipomoelin in complex with various carbohydrates MMP, MGP and sialic acid revealed its sugar binding properties
Date Issued
2010
Date
2010
Author(s)
Liu, Kai-Lun
Abstract
Ipomoelin (IPO) is a defense protein from sweet potato (Ipomoea batatas cv. Tainung 57) and will be induced by wounding, methyl jasmonate (MeJA), and ethylene. IPO belongs to Lectin family and it can bind various carbohydrates in different affinities. For investigating the binding modes of IPO for various carbohydrates, the purified proteins of native IPO, IPO in complex with methyl α-D-mannopyranoside (MMP), methyl α-D-glucopyranoside (MGP), sialic acid (SA) were respectively crystallized and resolved. They showed different space group after indexing and scaling. The native IPO is a space group I222 with unit-cell a=87.5 Å, b=139.5 Å, c=189.9 Å, α=β=γ=90º. The structure of native IPO was determined by molecular replacement method in CNS program using Calespa structure (pdb id: 1OUW) as search model. Finally, the crystal structure of IPO was resolved at a resolution 2.3 Å. The following complex structures of IPO with carbohydrates were crystallized in space group C2221 for IPO-MMP at 2.1 Å resolution, P21 for IPO-MGP at 2.1 Å resolution, and P41 for IPO-SA at 1.9 Å resolution, respectively. IPO consists of fourteen strands of β-sheet to form a β-prism structure and functions as tetramer. The carbohydrates MMP, MGP, and SA could be clearly observed in the binding pocket of IPO and contoured by the omitted map. In general, three carbohydrates, MMP, MGP and SA share three hydrogen-bonding interactions with Gly21, Trp142 and Asp145 of IPO. The atoms O3 and O4 of MMP form a network of four hydrogen bonds with IPO. Additionally, MGP and SA share two other hydrogen-bonding interactions with Tyr97 and Tyr143 of IPO. IPO have another hydrogen bond between Gly141 and MGP, and another hydrogen bond between Ser140 and SA. The results from IPO in complex with various carbohydrates will provide the further information of binding specificities in IPO from lower to higher affinity.
Subjects
ipomoelin
structure
crystallography
Type
thesis
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