spacer
spacer

PDBsum entry 1fk4

Go to PDB code: 
protein ligands links
Lipid transport PDB id
1fk4
Jmol
Contents
Protein chain
93 a.a. *
Ligands
STE
FMT ×2
Waters ×62
* Residue conservation analysis
PDB id:
1fk4
Name: Lipid transport
Title: Structural basis of non-specific lipid binding in maize lipid-transfer protein complexes with stearic acid revealed by high-resolution x-ray crystallography
Structure: Nonspecific lipid-transfer protein. Chain: a
Source: Zea mays. Organism_taxid: 4577
Resolution:
1.80Å     R-factor:   0.200     R-free:   0.208
Authors: G.W.Han,J.Y.Lee,H.K.Song,D.H.Shin,S.W.Suh
Key ref:
G.W.Han et al. (2001). Structural basis of non-specific lipid binding in maize lipid-transfer protein complexes revealed by high-resolution X-ray crystallography. J Mol Biol, 308, 263-278. PubMed id: 11327766 DOI: 10.1006/jmbi.2001.4559
Date:
09-Aug-00     Release date:   06-Jun-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P19656  (NLTP_MAIZE) -  Non-specific lipid-transfer protein
Seq:
Struc:
120 a.a.
93 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     apoplast   4 terms 
  Biological process     transport   2 terms 
  Biochemical function     lipid binding     2 terms  

 

 
DOI no: 10.1006/jmbi.2001.4559 J Mol Biol 308:263-278 (2001)
PubMed id: 11327766  
 
 
Structural basis of non-specific lipid binding in maize lipid-transfer protein complexes revealed by high-resolution X-ray crystallography.
G.W.Han, J.Y.Lee, H.K.Song, C.Chang, K.Min, J.Moon, D.H.Shin, M.L.Kopka, M.R.Sawaya, H.S.Yuan, T.D.Kim, J.Choe, D.Lim, H.J.Moon, S.W.Suh.
 
  ABSTRACT  
 
Non-specific lipid-transfer proteins (nsLTPs) are involved in the movement of phospholipids, glycolipids, fatty acids, and steroids between membranes. Several structures of plant nsLTPs have been determined both by X-ray crystallography and nuclear magnetic resonance. However, the detailed structural basis of the non-specific binding of hydrophobic ligands by nsLTPs is still poorly understood. In order to gain a better understanding of the structural basis of the non-specific binding of hydrophobic ligands by nsLTPs and to investigate the plasticity of the fatty acid binding cavity in nsLTPs, seven high-resolution (between 1.3 A and 1.9 A) crystal structures have been determined. These depict the nsLTP from maize seedlings in complex with an array of fatty acids.A detailed comparison of the structures of maize nsLTP in complex with various ligands reveals a new binding mode in an nsLTP-oleate complex which has not been seen before. Furthermore, in the caprate complex, the ligand binds to the protein cavity in two orientations with equal occupancy. The volume of the hydrophobic cavity in the nsLTP from maize shows some variation depending on the size of the bound ligands.The structural plasticity of the ligand binding cavity and the predominant involvement of non-specific van der Waals interactions with the hydrophobic tail of the ligands provide a structural explanation for the non-specificity of maize nsLTP. The hydrophobic cavity accommodates various ligands from C10 to C18. The C18:1 ricinoleate with its hydroxyl group hydrogen bonding to Ala68 possibly mimics cutin monomer binding which is of biological importance. Some of the myristate binding sites in human serum albumin resemble the maize nsLTP, implying the importance of a helical bundle in accommodating the non-specific binding of fatty acids.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) Stereo ribbon diagram of maize non-specific lipid-transfer protein complexed with oleate. The Figures were drawn with the MOLSCRIPT program.41 (b) Superposition of the backbone trace of eight nsLTP complexes. (c) Bound fatty acids showing structural comparisons between complexes. Colors used in (b) and (c): nsLTP:caprate (purple), nsLTP:laurate (red), nsLTP:myristate (dark red), nsLTP:palmitoleate (green), nsLTP-stearate (blue), nsLTP:oleate (dark green), nsLTP-linoleneate (yellow), and nsLTP-ricinoleate (dark blue).
Figure 6.
Figure 6. Comparisons of nsLTP:myristate with human serum albumin (HSA) in complex with myristate moieties. Insight II v97.5 (Molecular Simulations, Inc.) was used for the display. The three domains of HSA bind five myristate moieties; four are shown here, myr1, myr3, myr4, and myr5.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 308, 263-278) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21254439 Y.H.Ko, Y.Kim, H.Kim, and K.Kim (2011).
U-Shaped Conformation of Alkyl Chains Bound to a Synthetic Receptor Cucurbit[8]uril.
  Chem Asian J, 6, 652-657.  
20532958 H.W.Wang, H.J.Kwon, W.C.Yim, S.D.Lim, J.C.Moon, B.M.Lee, Y.W.Seo, W.Kim, and C.S.Jang (2010).
Expressional diversity of wheat nsLTP genes: evidence of subfunctionalization via cis-regulatory divergence.
  Genetica, 138, 843-852.  
20667964 K.Chae, B.J.Gonong, S.C.Kim, C.A.Kieslich, D.Morikis, S.Balasubramanian, and E.M.Lord (2010).
A multifaceted study of stigma/style cysteine-rich adhesin (SCA)-like Arabidopsis lipid transfer proteins (LTPs) suggests diversified roles for these LTPs in plant growth and reproduction.
  J Exp Bot, 61, 4277-4290.  
20419185 X.Xiao, J.X.Liu, Z.F.Fan, K.Chen, Q.J.Zhu, S.F.Xue, and Z.Tao (2010).
Chirality from achiral components: N,N'-bis(4-dimethylaminobenzyl)dodecane-1,12-diammonium in cucurbit[8]uril.
  Chem Commun (Camb), 46, 3741-3743.  
19308324 K.Teilum, J.G.Olsen, and B.B.Kragelund (2009).
Functional aspects of protein flexibility.
  Cell Mol Life Sci, 66, 2231-2247.  
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.  
18803664 C.Li, W.Xie, W.Bai, Z.Li, Y.Zhao, and H.Liu (2008).
Calmodulin binds to maize lipid transfer protein and modulates its lipids binding ability.
  FEBS J, 275, 5298-5308.  
18552128 M.B.Lascombe, B.Bakan, N.Buhot, D.Marion, J.P.Blein, V.Larue, C.Lamb, and T.Prangé (2008).
The structure of "defective in induced resistance" protein of Arabidopsis thaliana, DIR1, reveals a new type of lipid transfer protein.
  Protein Sci, 17, 1522-1530.
PDB code: 2rkn
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.  
17384226 E.J.Choi, J.Mao, and S.L.Mayo (2007).
Computational design and biochemical characterization of maize nonspecific lipid transfer protein variants for biosensor applications.
  Protein Sci, 16, 582-588.  
17609776 J.Rebek (2007).
Contortions of encapsulated alkyl groups.
  Chem Commun (Camb), (), 2777-2789.  
17878166 K.Chae, K.Zhang, L.Zhang, D.Morikis, S.T.Kim, J.C.Mollet, N.de la Rosa, K.Tan, and E.M.Lord (2007).
Two SCA (stigma/style cysteine-rich adhesin) isoforms show structural differences that correlate with their levels of in vitro pollen tube adhesion activity.
  J Biol Chem, 282, 33845-33858.  
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.  
16477037 B.W.Purse, and J.Rebek (2006).
Self-fulfilling cavitands: packing alkyl chains into small spaces.
  Proc Natl Acad Sci U S A, 103, 2530-2534.  
16177913 K.Liu, H.Jiang, S.L.Moore, C.B.Watkins, and M.M.Jahn (2006).
Isolation and characterization of a lipid transfer protein expressed in ripening fruit of Capsicum chinense.
  Planta, 223, 672-683.  
16739157 M.P.Schramm, and J.Rebek (2006).
Moving targets: recognition of alkyl groups.
  Chemistry, 12, 5924-5933.  
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.  
16432565 R.J.Hooley, S.M.Biros, and J.Rebek (2006).
Normal hydrocarbons tumble rapidly in a deep, water-soluble cavitand.
  Chem Commun (Camb), (), 509-510.  
15805594 F.Hoh, J.L.Pons, M.F.Gautier, F.de Lamotte, and C.Dumas (2005).
Structure of a liganded type 2 non-specific lipid-transfer protein from wheat and the molecular basis of lipid binding.
  Acta Crystallogr D Biol Crystallogr, 61, 397-406.
PDB code: 1tuk
16204887 J.Aishima, D.S.Russel, L.J.Guibas, P.D.Adams, and A.T.Brunger (2005).
Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface.
  Acta Crystallogr D Biol Crystallogr, 61, 1354-1363.  
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
15295114 H.C.Cheng, P.T.Cheng, P.Peng, P.C.Lyu, and Y.J.Sun (2004).
Lipid binding in rice nonspecific lipid transfer protein-1 complexes from Oryza sativa.
  Protein Sci, 13, 2304-2315.
PDB codes: 1uva 1uvb 1uvc
15583398 S.Y.Wang, K.J.Zhou, X.Y.Ye, Z.B.Xu, J.H.Wu, and P.F.Rao (2004).
Crystallization and preliminary X-ray crystallographic analysis of a non-specific lipid-transfer protein with antipathogenic activity from Phaseolus mungo.
  Acta Crystallogr D Biol Crystallogr, 60, 2391-2393.  
12680870 J.A.Asturias, N.Gómez-Bayón, J.L.Eseverri, and A.Martínez (2003).
Par j 1 and Par j 2, the major allergens from Parietaria judaica pollen, have similar immunoglobulin E epitopes.
  Clin Exp Allergy, 33, 518-524.  
12577257 U.Schulze-Gahmen, J.Pelaschier, H.Yokota, R.Kim, and S.H.Kim (2003).
Crystal structure of a hypothetical protein, TM841 of Thermotoga maritima, reveals its function as a fatty acid-binding protein.
  Proteins, 50, 526-530.
PDB code: 1mgp
12171654 D.K.Hincha (2002).
Cryoprotectin: a plant lipid-transfer protein homologue that stabilizes membranes during freezing.
  Philos Trans R Soc Lond B Biol Sci, 357, 909-916.  
12011089 D.Samuel, Y.J.Liu, C.S.Cheng, and P.C.Lyu (2002).
Solution structure of plant nonspecific lipid transfer protein-2 from rice (Oryza sativa).
  J Biol Chem, 277, 35267-35273.
PDB code: 1l6h
12171657 R.Lundheim (2002).
Physiological and ecological significance of biological ice nucleators.
  Philos Trans R Soc Lond B Biol Sci, 357, 937-943.  
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.