Rice non-specific lipid transfer protein: The 1.6 Å crystal structure in the unliganded state reveals a small hydrophobic cavity

Jae Young Lee, Kyeongsik Min, Hoon Cha, Dong Hae Shin, Kwang Yeon Hwang, Se Won Suh

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This study describes the high-resolution X-ray structure of the nonspecific lipid transfer protein (ns-LTP) from rice seeds in the unliganded state. The model has been refined to a crystallographic R-factor of 0.186 for 8.0 to 1.6 Å data (with F(o) > 2 σ(F)). It accounts for all 91 amino acid residues, 68 water molecules, one sulfate ion, and two molecules of 3-[cyclohexylamino]-1-propanesulfonic acid. The root-mean-square deviations from ideal bond lengths and angles are 0.017 Å and 1.76°, respectively. The overall fold of rice ns-LTP is very similar to that of maize ns-LTP. A superposition of 91 common C(α) atoms in rice and maize ns-LTPs, both in the unliganded state, gives a root-mean-square deviation of 1.2 Å. Large structural differences from the crystal structure of maize ns-LTP are observed in two regions: the loop between two α-helices H1 and H2, where one residue deletion (Gln21 of maize sequence) occurs, and the C-terminal region around Tyr79. The C-terminal region of rice protein is somewhat collapsed into the hydrophobic cavity. As a consequence, its hydrophobic cavity is considerably smaller than that of maize protein (144 Å3 versus 408 Å3 for van der Waals cavity volumes), despite a high level of sequence identity (79%) between them. In the rice ns-LTP structure, the side-chain of Arg44 partially blocks the mouth of the cavity, while the side-chain of Ile81 effectively closes the other end by protruding into the cavity. And the side-chain of Tyr79 divides the cavity into two parts, with the larger part being shielded from the solvent. The present study illuminates the structure-function relationship of rice ns-LTP and allows a detailed structural comparison with other plant ns-LTPs.

Original languageEnglish
Pages (from-to)437-448
Number of pages12
JournalJournal of Molecular Biology
Issue number2
StatePublished - 20 Feb 1998

Bibliographical note

Funding Information:
We thank Professor J.-C. Kader and his co-workers for establishing the lipid transfer activity of rice PAPI. We thank the Inter-University Center for Natural Science Research Facilities for providing the X-ray equipment. This work was supported by the Korea Science and Engineering Foundation International Cooperative Research grant (1994–1996), Korea Ministry of Education Basic Sciences Research Institute grant, a grant from the Center for Molecular Catalysis, Seoul National University, and S.N.U. Dae Woo Research Fund (97-05-2073).


  • Crystal structure
  • Hydrophobic cavity
  • Non-specific lipid transfer protein
  • Probable amylase/protease inhibitor
  • Rice protein


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