1UGY

Crystal structure of jacalin- mellibiose (Gal-alpha(1-6)-Glc) complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural Basis of the Carbohydrate Specificities of Jacalin: An X-ray and Modeling Study

Jeyaprakash, A.A.Katiyar, S.Swaminathan, C.P.Sekar, K.Surolia, A.Vijayan, M.

(2003) J Mol Biol 332: 217-228

  • DOI: 10.1016/s0022-2836(03)00901-x
  • Primary Citation of Related Structures:  
    1UGY, 1UGX, 1UGW, 1UH1, 1UH0

  • PubMed Abstract: 
  • The structures of the complexes of tetrameric jacalin with Gal, Me-alpha-GalNAc, Me-alpha-T-antigen, GalNAcbeta1-3Gal-alpha-O-Me and Galalpha1-6Glc (mellibiose) show that the sugar-binding site of jacalin has three components: the primary site, secondary site A, and secondary site B ...

    The structures of the complexes of tetrameric jacalin with Gal, Me-alpha-GalNAc, Me-alpha-T-antigen, GalNAcbeta1-3Gal-alpha-O-Me and Galalpha1-6Glc (mellibiose) show that the sugar-binding site of jacalin has three components: the primary site, secondary site A, and secondary site B. In these structures and in the two structures reported earlier, Gal or GalNAc occupy the primary site with the anomeric carbon pointing towards secondary site A. The alpha-substituents, when present, interact, primarily hydrophobically, with secondary site A which has variable geometry. O-H..., centered pi and C-H...pi hydrogen bonds involving this site also exist. On the other hand, beta-substitution leads to severe steric clashes. Therefore, in complexes involving beta-linked disaccharides, the reducing sugar binds at the primary site with the non-reducing end located at secondary site B. The interactions at secondary site B are primarily through water bridges. Thus, the nature of the linkage determines the mode of the association of the sugar with jacalin. The interactions observed in the crystal structures and modeling based on them provide a satisfactory qualitative explanation of the available thermodynamic data on jacalin-carbohydrate interactions. They also lead to fresh insights into the nature of the binding of glycoproteins by jacalin.


    Related Citations: 
    • Crystal structure of the jacalin-T-antigen complex and a comparative study of lectin-T-antigen complexes
      Jeyaprakash, A.A., Rani, P.G., Reddy, G.B., Banumathi, S., Betzel, C., Sekar, K., Surolia, A., Vijayan, M.
      (2002) J Mol Biol 321: 637
    • A Novel mode of carbohydrate recognition in jacalin, A moraceae plant lectin with a beta-prism fold
      Sankaranarayanan, R., Sekar, K., Banerjee, R., Sharma, V., Surolia, A., Vijayan, M.
      (1996) Nat Struct Biol 3: 596

    Organizational Affiliation

    Molecular Biophysics Unit, UGC Centre of Advanced Study, Indian Institute of Science, Bangalore 560 012, India.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Agglutinin alpha chainA, G133Artocarpus integerMutation(s): 0 
UniProt
Find proteins for P18670 (Artocarpus integer)
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Go to UniProtKB:  P18670
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Agglutinin beta-3 chainB, D, F, H20Artocarpus integerMutation(s): 0 
UniProt
Find proteins for P18673 (Artocarpus integer)
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Go to UniProtKB:  P18673
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Agglutinin alpha chainC, E133Artocarpus integerMutation(s): 0 
UniProt
Find proteins for P18670 (Artocarpus integer)
Explore P18670 
Go to UniProtKB:  P18670
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-6)-alpha-D-glucopyranoseI, J2 N/A Oligosaccharides Interaction
Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-6)-beta-D-glucopyranoseK, L2 N/A Oligosaccharides Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900037
Query on PRD_900037
I, Jalpha-melibioseOligosaccharide /  Metabolism Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.46α = 90
b = 99.83β = 90
c = 105.65γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary