2GSJ

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

• PDB DOI: https://doi.org/10.2210/pdb2GSJ/pdb

• Classification: HYDROLASE
• Organism(s): Parkia platycephala
• Mutation(s): No 


• Deposited: 2006-04-26 Released: 2007-03-13 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

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

• PubMed: 16934035 
• DOI: https://doi.org/10.1111/j.1742-4658.2006.05400.x
• Primary Citation of Related Structures:  
  2GSJ


• 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.

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Organizational Affiliation: 

BioMol-Laboratory, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.9 kDa 
• Atom Count: 2,355 
• Modelled Residue Count: 271 
• Deposited Residue Count: 271 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein PPL-2	A	271	Parkia platycephala	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.19	α = 90
b = 59.949	β = 90
c = 76.697	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-13 
Deposition Author(s): 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.

Revision History  

• 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
• Version 1.4: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary