PDBsum entry 2gl1

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protein links
Plant protein PDB id
Protein chain
47 a.a. *
* Residue conservation analysis
PDB id:
Name: Plant protein
Title: Nmr solution structure of vigna radiata defensin 2 (vrd2)
Structure: Pdf1. Chain: a. Fragment: residues 1-47. Synonym: defensin 2
Source: Vigna radiata. Organism_taxid: 157791
NMR struc: 18 models
Authors: K.F.Lin,T.R.Lee,P.H.Tsai,M.P.Hsu,C.S.Chen,P.C.Lyu
Key ref:
K.F.Lin et al. (2007). Structure-based protein engineering for alpha-amylase inhibitory activity of plant defensin. Proteins, 68, 530-540. PubMed id: 17444520 DOI: 10.1002/prot.21378
04-Apr-06     Release date:   03-Apr-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q8W434  (Q8W434_VIGRA) -  PDF1
75 a.a.
47 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     defense response   1 term 


DOI no: 10.1002/prot.21378 Proteins 68:530-540 (2007)
PubMed id: 17444520  
Structure-based protein engineering for alpha-amylase inhibitory activity of plant defensin.
K.F.Lin, T.R.Lee, P.H.Tsai, M.P.Hsu, C.S.Chen, P.C.Lyu.
The structure of a novel plant defensin isolated from the seeds of the mung bean, Vigna radiate, has been determined by (1)H nuclear magnetic resonance spectroscopy. The three-dimensional structure of VrD2, the V. radiate plant defensin 2 protein, comprises an alpha-helix and one triple-stranded anti-parallel beta-sheet stabilized by four disulfide bonds. This protein exhibits neither insecticidal activity nor alpha-amylase inhibitory activity in spite of showing a similar global fold to that of VrD1, an insecticidal plant defensin that has been suggested to function by inhibiting insect alpha-amylase. Our previous study proposed that loop L3 of plant defensins is important for this inhibition. Structural analyses and surface charge comparisons of VrD1 and VrD2 revealed that the charged residues of L3 correlate with the observed difference in inhibitory activities of these proteins. A VrD2 chimera that was produced by transferring the proposed functional loop of VrD1 onto the structurally equivalent loop of VrD2 supported this hypothesis. The VrD2 chimera, which differs by only five residues compared with VrD2, showed obvious activity against Tenebrio molitor alpha-amylase. These results clarify the mode of alpha-amylase inhibition of plant defensins and also represent a possible approach for engineering novel alpha-amylase inhibitors. Plant defensins are important constituents of the innate immune system of plants, and thus the application of protein engineering to this protein family may provide an efficient method for protecting against crop losses.
  Selected figure(s)  
Figure 4.
Figure 4. Structural comparisons of VrD1 and VrD2. A: The structures of VrD1 (PDB id: 1TI5) and VrD2 (PDB id: 2GL1) were superimposed on the backbone atoms of the secondary structural elements by Swiss-PdbViewer 3.7[78] and colored in green and red, respectively. B: The orientation of residues Asp^37-Arg^40 of VrD2 and Arg^38 of VrD1. The structure in (B) is rotated by 90° around its x-axis compared with that in (A). These figures are produced using Accelrys DS ViewerPro (DiscoveryStudio. San Diego, CA: Accelrys Ins; 2002).
Figure 5.
Figure 5. A: Putative model of the TMA-VrD2c complex. The surfaces of VrD2c and TMA are colored in blue and orange, respectively. B: Loop L3 of VrD2c was shown to dock in the TMA active site to prevent substrate binding. VrD2c is shown as cartoon and colored in green. The figure and the electrostatic surface potential of TMA were computed by PyMOL.[79] C: The surface charge distribution of TMA, VrD1, VrD2, and VrD2c. The electrostatic potential is indicated in red (negative charge), white (neutral), and blue (positive charge).
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2007, 68, 530-540) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19422058 T.Chen, T.R.Lee, W.G.Liang, W.S.Chang, and P.C.Lyu (2009).
Identification of trypsin-inhibitory site and structure determination of human SPINK2 serine proteinase inhibitor.
  Proteins, 77, 209-219.
PDB code: 2jxd
19533758 Y.F.Yang, K.C.Cheng, P.H.Tsai, C.C.Liu, T.R.Lee, and P.C.Lyu (2009).
Alanine substitutions of noncysteine residues in the cysteine-stabilized alphabeta motif.
  Protein Sci, 18, 1498-1506.  
18498107 P.B.Pelegrini, F.T.Lay, A.M.Murad, M.A.Anderson, and O.L.Franco (2008).
Novel insights on the mechanism of action of alpha-amylase inhibitors from the plant defensin family.
  Proteins, 73, 719-729.  
18726095 S.Vijayan, L.Guruprasad, and P.B.Kirti (2008).
Prokaryotic expression of a constitutively expressed Tephrosia villosa defensin and its potent antifungal activity.
  Appl Microbiol Biotechnol, 80, 1023-1032.  
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.