cDNA cloning and 1.75A crystal structure determination of PPL2, a novel chimerolectin from Parkia platycephala seeds exhibiting endochitinolytic activity

Experimental Data Snapshot

  • Resolution: 1.73 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.175 

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cDNA cloning and 1.75 A crystal structure determination of PPL2, an endochitinase and N-acetylglucosamine-binding hemagglutinin from Parkia platycephala seeds

Cavada, B.S.Moreno, F.B.da Rocha, B.A.de Azevedo Jr., W.F.Castellon, R.E.R.Goersch, G.V.Nagano, C.S.de Souza, E.P.Nascimento, K.S.Radis-Baptista, G.Delatorre, P.Leroy, Y.Toyama, M.H.Pinto, V.P.Sampaio, A.H.Barettino, D.Debray, H.Calvete, J.J.Sanz, L.

(2006) FEBS J 273: 3962-3974

  • DOI: https://doi.org/10.1111/j.1742-4658.2006.05400.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Parkia platycephala lectin 2 was purified from Parkia platycephala (Leguminosae, Mimosoideae) seeds by affinity chromatography and RP-HPLC. Equilibrium sedimentation and MS showed that Parkia platycephala lectin 2 is a nonglycosylated monomeric protein of molecular mass 29 407+/-15 Da, which contains six cysteine residues engaged in the formation of three intramolecular disulfide bonds. Parkia platycephala lectin 2 agglutinated rabbit erythrocytes, and this activity was specifically inhibited by N-acetylglucosamine. In addition, Parkia platycephala lectin 2 hydrolyzed beta(1-4) glycosidic bonds linking 2-acetoamido-2-deoxy-beta-D-glucopyranose units in chitin. The full-length amino acid sequence of Parkia platycephala lectin 2, determined by N-terminal sequencing and cDNA cloning, and its three-dimensional structure, established by X-ray crystallography at 1.75 A resolution, showed that Parkia platycephala lectin 2 is homologous to endochitinases of the glycosyl hydrolase family 18, which share the (betaalpha)8 barrel topology harboring the catalytic residues Asp125, Glu127, and Tyr182.

  • Organizational Affiliation

    BioMol-Laboratory, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil. bscavada@ufc.br

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
protein PPL-2271Parkia platycephalaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.73 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.19α = 90
b = 59.949β = 90
c = 76.697γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description