PDBsum entry 1uva

Lipid transport

PDB id

1uva

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Contents

			Protein chain

					91 a.a. *

			Ligands

					MYR

			Waters ×90

* Residue conservation analysis

PDB id:

1uva

Links

Name:

Lipid transport

Title:

Lipid binding in rice nonspecific lipid transfer protein-1 complexes from oryza sativa

Structure:

Nonspecific lipid transfer protein 1. Chain: a. Synonym: ltp 1, pap 1. Other_details: complexed with myristic acid

Source:

Oryza sativa. Rice. Organism_taxid: 4530

Biol. unit:

Dimer (from PDB file)

Resolution:

2.50Å

R-factor:

0.216

R-free:

0.288

Authors:

H.-C.Cheng,P.-T.Cheng,P.Peng,P.-C.Lyu,Y.-J.Sun

Key ref:

H.C.Cheng et al. (2004). Lipid binding in rice nonspecific lipid transfer protein-1 complexes from Oryza sativa. Protein Sci, 13, 2304-2315. PubMed id: 15295114 DOI: 10.1110/ps.04799704

Date:

19-Jan-04

Release date:

19-Oct-04

PROCHECK

	Headers

	References

Protein chain

Q0IQK9 (NLTP1_ORYSJ) - Non-specific lipid-transfer protein 1 from Oryza sativa subsp. japonica

Seq: Struc:					116 a.a. 91 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

DOI no: 10.1110/ps.04799704	Protein Sci 13:2304-2315 (2004)
PubMed id: 15295114

Lipid binding in rice nonspecific lipid transfer protein-1 complexes from Oryza sativa.
H.C.Cheng, P.T.Cheng, P.Peng, P.C.Lyu, Y.J.Sun.

ABSTRACT

Nonspecific lipid transfer proteins (nsLTPs) facilitate the transfer of phospholipids, glycolipids, fatty acids and steroids between membranes, with wide-ranging binding affinities. Three crystal structures of rice nsLTP1 from Oryza sativa, complexed with myristic (MYR), palmitic (PAL) or stearic acid (STE) were determined. The overall structures of the rice nsLTP1 complexes belong to the four-helix bundle folding with a long C-terminal loop. The nsLTP1-MYR and the nsLTP1-STE complexes bind a single fatty acid while the nsLTP1-PAL complex binds two molecules of fatty acids. The C-terminal loop region is elastic in order to accommodate a diverse range of lipid molecules. The lipid molecules interact with the nsLTP1-binding cavity mainly with hydrophobic interactions. Significant conformational changes were observed in the binding cavity and the C-terminal loop of the rice nsLTP1 upon lipid binding.

Selected figure(s)



	Figure 4. Figure 4. (A-D) The molecular surface of the rice nsTLP1 complexes (nsLTP1-MYR, nsLTP1-PAL1 & 2, and nsLTP1-STE A & B) drawn by DS ViewerPro, colored according to the electrostatic potential, ranging from blue to red (-10.0 to +10.0). Residues 77-82 were removed to show the hydrophobic cavity. Labeled residues are those of rice nsLTP1 participating in hydrophobic interactions between protein and fatty acids as shown in Table 1 Go-. (E-H) A representation of the hydrophobic interactions between rice nsLTP1 and fatty acids (MYR, PAL, STE A, and STE B) by LIGPLOT (Wallace et al. 1995).		Figure 5. Figure 5. Hydrogen bond interactions between the head group of fatty acid and the rice nsLTP1: (A) the myristic acid (MYR) in the nsLTP1-MYR complex, (B) the first palmitic acid (PAL1) in the nsLTP1-PAL complex, (C) the second palmitic acid (PAL2) in the nsLTP1-PAL complex, and (D) the stearic acid (STE B) in the nsLTP1-STE complex.

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

20610705

D.Zhang, W.Liang, C.Yin, J.Zong, F.Gu, and D.Zhang (2010).
OsC6, encoding a lipid transfer protein, is required for postmeiotic anther development in rice.

Plant Physiol, 154, 149-162.

19236482

R.González-Rioja, J.A.Asturias, A.Martínez, F.M.Goñi, and A.R.Viguera (2009).
Par j 1 and Par j 2, the two major allergens in Parietaria judaica, bind preferentially to monoacylated negative lipids.

FEBS J, 276, 1762-1775.

17891402

C.Wang, W.Xie, F.Chi, W.Hu, G.Mao, D.Sun, C.Li, and Y.Sun (2008).
BcLTP, a novel lipid transfer protein in Brassica chinensis, may secrete and combine extracellular CaM.

Plant Cell Rep, 27, 159-169.

18096636

T.H.Yeats, and J.K.Rose (2008).
The biochemistry and biology of extracellular plant lipid-transfer proteins (LTPs).

Protein Sci, 17, 191-198.

18338386

Y.T.Lai, C.S.Cheng, Y.N.Liu, Y.J.Liu, and P.C.Lyu (2008).
Effects of ligand binding on the dynamics of rice nonspecific lipid transfer protein 1: a model from molecular simulations.

Proteins, 72, 1189-1198.

17997832

L.Dvoráková, F.Cvrcková, and L.Fischer (2007).
Analysis of the hybrid proline-rich protein families from seven plant species suggests rapid diversification of their sequences and expression patterns.

BMC Genomics, 8, 412.

16555311

P.Da Silva, C.Landon, R.Beltoise, M.Ponchet, and F.Vovelle (2006).
Accessibility of tobacco lipid transfer protein cavity revealed by 15N NMR relaxation studies and molecular dynamics simulations.

Proteins, 64, 124-132.

15726627

P.Da Silva, C.Landon, B.Industri, A.Marais, D.Marion, M.Ponchet, and F.Vovelle (2005).
Solution structure of a tobacco lipid transfer protein exhibiting new biophysical and biological features.

Proteins, 59, 356-367.

PDB code:

1t12

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.