1BWU

MANNOSE-SPECIFIC AGGLUTININ (LECTIN) FROM GARLIC (ALLIUM SATIVUM) BULBS COMPLEXED WITH ALPHA-D-MANNOSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of a dimeric mannose-specific agglutinin from garlic: quaternary association and carbohydrate specificity.

Chandra, N.R.Ramachandraiah, G.Bachhawat, K.Dam, T.K.Surolia, A.Vijayan, M.

(1999) J.Mol.Biol. 285: 1157-1168

  • DOI: 10.1006/jmbi.1998.2353

  • PubMed Abstract: 
  • A mannose-specific agglutinin, isolated from garlic bulbs, has been crystallized in the presence of a large excess of alpha-d-mannose, in space group C2 and cell dimensions, a=203.24, b=43.78, c=79.27 A, beta=112.4 degrees, with two dimers in the asy ...

    A mannose-specific agglutinin, isolated from garlic bulbs, has been crystallized in the presence of a large excess of alpha-d-mannose, in space group C2 and cell dimensions, a=203.24, b=43.78, c=79.27 A, beta=112.4 degrees, with two dimers in the asymmetric unit. X-ray diffraction data were collected up to a nominal resolution of 2.4 A and the structure was solved by molecular replacement. The structure, refined to an R-factor of 22.6 % and an Rfree of 27.8 % reveals a beta-prism II fold, similar to that in the snowdrop lectin, comprising three antiparallel four-stranded beta-sheets arranged as a 12-stranded beta-barrel, with an approximate internal 3-fold symmetry. This agglutinin is, however, a dimer unlike snowdrop lectin which exists as a tetramer, despite a high degree of sequence similarity between them. A comparison of the two structures reveals a few substitutions in the garlic lectin which stabilise it into a dimer and prevent tetramer formation. Three mannose molecules have been identified on each subunit. In addition, electron density is observed for another possible mannose molecule per dimer resulting in a total of seven mannose molecules in each dimer. Although the mannose binding sites and the overall structure are similar in the subunits of snowdrop and garlic lectin, their specificities to glycoproteins such as GP120 vary considerably. These differences appear, in part, to be a direct consequence of the differences in oligomerisation, implying that variation in quaternary association may be a mode of achieving oligosaccharide specificity in bulb lectins.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Studies on the Mannose- Specific Lectin from Garlic
      Chandra, N.R.,Dam, T.K.,Surolia, A.,Vijayan, M.
      (1997) Acta Crystallogr.,Sect.D 53: 787


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (AGGLUTININ)
A
106Allium sativumGene Names: LECASAI3
Find proteins for Q38789 (Allium sativum)
Go to UniProtKB:  Q38789
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (AGGLUTININ)
D
109Allium sativumGene Names: ASAII2
Find proteins for Q38784 (Allium sativum)
Go to UniProtKB:  Q38784
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (AGGLUTININ)
P
106Allium sativumGene Names: LECASAI3
Find proteins for Q38789 (Allium sativum)
Go to UniProtKB:  Q38789
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (AGGLUTININ)
Q
109Allium sativumGene Names: ASAII2
Find proteins for Q38784 (Allium sativum)
Go to UniProtKB:  Q38784
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, D, P, Q
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.226 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 203.243α = 90.00
b = 43.780β = 112.37
c = 79.268γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
X-PLORrefinement
AUTOMARdata reduction
AMoREphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description