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PDBsum entry 1afh

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protein links
Lipid-binding protein PDB id
1afh
Jmol
Contents
Protein chain
93 a.a. *
* Residue conservation analysis
PDB id:
1afh
Name: Lipid-binding protein
Title: Lipid transfer protein from maize seedlings, nmr, 15 structures
Structure: Maize nonspecific lipid transfer protein. Chain: a
Source: Zea mays. Organism_taxid: 4577. Organ: seeds
NMR struc: 15 models
Authors: J.Gomar,M.C.Petit,P.Sodano,D.Sy,D.Marion,J.C.Kader, F.Vovelle,M.Ptak
Key ref:
J.Gomar et al. (1996). Solution structure and lipid binding of a nonspecific lipid transfer protein extracted from maize seeds. Protein Sci, 5, 565-577. PubMed id: 8845747 DOI: 10.1002/pro.5560050402
Date:
07-Mar-97     Release date:   15-May-97    
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!
  Biological process     transport   2 terms 
  Biochemical function     lipid binding     1 term  

 

 
DOI no: 10.1002/pro.5560050402 Protein Sci 5:565-577 (1996)
PubMed id: 8845747  
 
 
Solution structure and lipid binding of a nonspecific lipid transfer protein extracted from maize seeds.
J.Gomar, M.C.Petit, P.Sodano, D.Sy, D.Marion, J.C.Kader, F.Vovelle, M.Ptak.
 
  ABSTRACT  
 
The three-dimensional solution structure of a nonspecific lipid transfer protein extracted from maize seeds determined by 1H NMR spectroscopy is described. This cationic protein consists of 93 amino acid residues. Its structure was determined from 1,091 NOE-derived distance restraints, including 929 interresidue connectivities and 197 dihedral restraints (phi, psi, chi 1) derived from NOEs and 3J coupling constants. The global fold involving four helical fragments connected by three loops and a C-terminal tail without regular secondary structures is stabilized by four disulfide bridges. The most striking feature of this structure is the existence of an internal hydrophobic cavity running through the whole molecule. The global fold of this protein, very similar to that of a previously described lipid transfer protein extracted from wheat seeds (Gincel E et al., 1994, Eur J Biochem 226:413-422) constitutes a new architecture for alpha-class proteins. 1H NMR and fluorescence studies show that this protein forms well-defined complexes in aqueous solution with lysophosphatidylcholine. Dissociation constants, Kd, of 1.9 +/- 0.6 x 10(-6) M and > 10(-3) M were obtained with lyso-C16 and -C12, respectively. A structure model for a lipid-protein complex is proposed in which the aliphatic chain of the phospholipid is inserted in the internal cavity and the polar head interacts with the charged side chains located at one end of this cavity. Our model for the lipid-protein complex is qualitatively very similar to the recently published crystal structure (Shin DH et al., 1995, Structure 3:189-199).
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Stereo view of the pore throughthe maize ns-LTP. The backbone isrepresented as a tube colored in cyan, hydrophobic residues lining the cavity are colored in yellow, basic residuesin pink, acidic residuesin blue, Tyr 17 and Tyr 81 in green, cys- teinesresiduesinblue-green,andpinkcirclesshowthesurface of thecavity,calculatedwithth PORE program(Smartet al., 1993).
Figure 10.
Fig. 10. Sequencealignment of HPS,wheat.andmaizens-LPT.Secondarystructureelementsareindicated.Arrowcorresponds IO a 8-strand.
 
  The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (1996, 5, 565-577) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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.  
18461470 X.Wang, H.Wang, Y.Li, K.Cao, and X.Ge (2009).
A rice lipid transfer protein binds to plasma membrane proteinaceous sites.
  Mol Biol Rep, 36, 745-750.  
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.  
18257684 J.Y.Sun, D.A.Gaudet, Z.X.Lu, M.Frick, B.Puchalski, and A.Laroche (2008).
Characterization and antifungal properties of wheat nonspecific lipid transfer proteins.
  Mol Plant Microbe Interact, 21, 346-360.  
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.  
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.  
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.  
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
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
16170781 Y.C.Chen, and J.K.Hwang (2005).
Prediction of disulfide connectivity from protein sequences.
  Proteins, 61, 507-512.  
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.  
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.  
12171657 R.Lundheim (2002).
Physiological and ecological significance of biological ice nucleators.
  Philos Trans R Soc Lond B Biol Sci, 357, 937-943.  
11274467 C.Landon, P.Berthault, F.Vovelle, and H.Desvaux (2001).
Magnetization transfer from laser-polarized xenon to protons located in the hydrophobic cavity of the wheat nonspecific lipid transfer protein.
  Protein Sci, 10, 762-770.  
11585909 M.D.Esposti, J.T.Erler, J.A.Hickman, and C.Dive (2001).
Bid, a widely expressed proapoptotic protein of the Bcl-2 family, displays lipid transfer activity.
  Mol Cell Biol, 21, 7268-7276.  
11532009 V.Campanacci, A.Mosbah, O.Bornet, R.Wechselberger, E.Jacquin-Joly, C.Cambillau, H.Darbon, and M.Tegoni (2001).
Chemosensory protein from the moth Mamestra brassicae. Expression and secondary structure from 1H and 15N NMR.
  Eur J Biochem, 268, 4731-4739.  
10713993 M.J.Pandya, R.B.Sessions, P.B.Williams, C.E.Dempsey, A.S.Tatham, P.R.Shewry, and A.R.Clarke (2000).
Structural characterization of a methionine-rich, emulsifying protein from sunflower seed.
  Proteins, 38, 341-349.  
10672021 S.Tassin-Moindrot, A.Caille, J.P.Douliez, D.Marion, and F.Vovelle (2000).
The wide binding properties of a wheat nonspecific lipid transfer protein. Solution structure of a complex with prostaglandin B2.
  Eur J Biochem, 267, 1117-1124.
PDB code: 1cz2
10491104 D.Charvolin, J.P.Douliez, D.Marion, C.Cohen-Addad, and E.Pebay-Peyroula (1999).
The crystal structure of a wheat nonspecific lipid transfer protein (ns-LTP1) complexed with two molecules of phospholipid at 2.1 A resolution.
  Eur J Biochem, 264, 562-568.
PDB code: 1bwo
10571986 F.Guerbette, M.Grosbois, A.Jolliot-Croquin, J.C.Kader, and A.Zachowski (1999).
Comparison of lipid binding and transfer properties of two lipid transfer proteins from plants.
  Biochemistry, 38, 14131-14137.  
10092854 J.Poznanski, P.Sodano, S.W.Suh, J.Y.Lee, M.Ptak, and F.Vovelle (1999).
Solution structure of a lipid transfer protein extracted from rice seeds. Comparison with homologous proteins.
  Eur J Biochem, 259, 692-708.
PDB code: 1bv2
10103017 V.Lullien-Pellerin, C.Devaux, T.Ihorai, D.Marion, V.Pahin, P.Joudrier, and M.F.Gautier (1999).
Production in Escherichia coli and site-directed mutagenesis of a 9-kDa nonspecific lipid transfer protein from wheat.
  Eur J Biochem, 260, 861-868.  
9593190 J.Gomar, P.Sodano, D.Sy, D.H.Shin, J.Y.Lee, S.W.Suh, D.Marion, F.Vovelle, and M.Ptak (1998).
Comparison of solution and crystal structures of maize nonspecific lipid transfer protein: a model for a potential in vivo lipid carrier protein.
  Proteins, 31, 160-171.  
  9865943 M.H.Lerche, and F.M.Poulsen (1998).
Solution structure of barley lipid transfer protein complexed with palmitate. Two different binding modes of palmitate in the homologous maize and barley nonspecific lipid transfer proteins.
  Protein Sci, 7, 2490-2498.
PDB code: 1be2
9521681 S.Tassin, W.F.Broekaert, D.Marion, D.P.Acland, M.Ptak, F.Vovelle, and P.Sodano (1998).
Solution structure of Ace-AMP1, a potent antimicrobial protein extracted from onion seeds. Structural analogies with plant nonspecific lipid transfer proteins.
  Biochemistry, 37, 3623-3637.  
9675898 Z.Keresztessy, and M.A.Hughes (1998).
Homology modelling and molecular dynamics aided analysis of ligand complexes demonstrates functional properties of lipid-transfer proteins encoded by the barley low-temperature-inducible gene family, blt4.
  Plant J, 14, 523-533.  
8961930 M.Rico, M.Bruix, C.González, R.I.Monsalve, and R.Rodríguez (1996).
1H NMR assignment and global fold of napin BnIb, a representative 2S albumin seed protein.
  Biochemistry, 35, 15672-15682.
PDB code: 1pnb
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.