6FLY

Structure of AcmJRL, a mannose binding jacalin related lectin from Ananas comosus, in complex with mannose.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

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This is version 1.1 of the entry. See complete history


Literature

Biochemical and structural characterization of a mannose binding jacalin-related lectin with two-sugar binding sites from pineapple (Ananas comosus) stem.

Azarkan, M.Feller, G.Vandenameele, J.Herman, R.El Mahyaoui, R.Sauvage, E.Vanden Broeck, A.Matagne, A.Charlier, P.Kerff, F.

(2018) Sci Rep 8: 11508-11508

  • DOI: 10.1038/s41598-018-29439-x
  • Primary Citation of Related Structures:  
    6FLW, 6FLY, 6FLZ

  • PubMed Abstract: 
  • A mannose binding jacalin-related lectin from Ananas comosus stem (AcmJRL) was purified and biochemically characterized. This lectin is homogeneous according to native, SDS-PAGE and N-terminal sequencing and the theoretical molecular mass was confirmed by ESI-Q-TOF-MS ...

    A mannose binding jacalin-related lectin from Ananas comosus stem (AcmJRL) was purified and biochemically characterized. This lectin is homogeneous according to native, SDS-PAGE and N-terminal sequencing and the theoretical molecular mass was confirmed by ESI-Q-TOF-MS. AcmJRL was found homodimeric in solution by size-exclusion chromatography. Rat erythrocytes are agglutinated by AcmJRL while no agglutination activity is detected against rabbit and sheep erythrocytes. Hemagglutination activity was found more strongly inhibited by mannooligomannosides than by D-mannose. The carbohydrate-binding specificity of AcmJRL was determined in some detail by isothermal titration calorimetry. All sugars tested were found to bind with low affinity to AcmJRL, with K a values in the mM range. In agreement with hemagglutination assays, the affinity increased from D-mannose to di-, tri- and penta-mannooligosaccharides. Moreover, the X-ray crystal structure of AcmJRL was obtained in an apo form as well as in complex with D-mannose and methyl-α-D-mannopyranoside, revealing two carbohydrate-binding sites per monomer similar to the banana lectin BanLec. The absence of a wall separating the two binding sites, the conformation of β7β8 loop and the hemagglutinating activity are reminiscent of the BanLec His84Thr mutant, which presents a strong anti-HIV activity in absence of mitogenic activity.


    Organizational Affiliation

    Laboratory of crystallography, Center for Protein Engineering-InBioS, B5a, University of Liège, 4000, Liège, Belgium. fkerff@ulg.ac.be.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Jacalin-like lectinA, B144Ananas comosusMutation(s): 0 
Gene Names: LOC109719601
UniProt
Find proteins for Q53J09 (Ananas comosus)
Explore Q53J09 
Go to UniProtKB:  Q53J09
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53J09
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.68α = 90
b = 86.68β = 90
c = 257.27γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
FRS-FNRSBelgiumIISN 4.4503.11
FRS-FNRSBelgiumMIS F.4518.12

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary