title: Rice non-specific lipid transfer protein: the 1.6 A crystal structure in the unliganded state reveals a small hydrophobic cavity.
abstract: This study describes the high-resolution X-ray structure of the non-specific 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 A data (with Fo > 2 sigma 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 A and 1.76 degrees, respectively. The overall fold of rice ns-LTP is very similar to that of maize ns-LTP. A superposition of 91 common C alpha atoms in rice and maize ns-LTPs, both in the unliganded state, gives a root-mean-square deviation of 1.2 A. Large structural differences from the crystal structure of maize ns-LTP are observed in two regions: the loop between two alpha-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 A3 versus 408 A3 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.
authors.affiliation: Department of Chemistry, College of Natural Sciences, Seoul National University, Korea.
authors.forename: J Y
authors.initials: JY
authors.lastname: Lee
authors.forename: K
authors.initials: K
authors.lastname: Min
authors.forename: H
authors.initials: H
authors.lastname: Cha
authors.forename: D H
authors.initials: DH
authors.lastname: Shin
authors.forename: K Y
authors.initials: KY
authors.lastname: Hwang
authors.forename: S W
authors.initials: SW
authors.lastname: Suh
mesh_terms: D000595:Amino Acid Sequence; D002352:Carrier Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D012275:Oryza / Q000737:chemistry*; D010940:Plant Proteins / Q000737:chemistry*; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid
chemical_list: D002352:Carrier Proteins; D010940:Plant Proteins; C072087:sterol carrier proteins