2GSJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1111/j.1742-4658.2006.05400.x

  • 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 prote ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
protein PPL-2
A
271N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.190α = 90.00
b = 59.949β = 90.00
c = 76.697γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
SCALAdata scaling
MAR345data collection
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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