1BCJ

MANNOSE-BINDING PROTEIN-A MUTANT (QPDWGHV) COMPLEXED WITH N-ACETYL-D-GALACTOSAMINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mechanism of N-acetylgalactosamine binding to a C-type animal lectin carbohydrate-recognition domain.

Kolatkar, A.R.Leung, A.K.Isecke, R.Brossmer, R.Drickamer, K.Weis, W.I.

(1998) J Biol Chem 273: 19502-19508

  • DOI: 10.1074/jbc.273.31.19502
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The mammalian hepatic asialoglycoprotein receptor, a member of the C-type animal lectin family, displays preferential binding to N-acetylgalactosamine compared with galactose. The structural basis for selective binding to N-acetylgalactosamine has be ...

    The mammalian hepatic asialoglycoprotein receptor, a member of the C-type animal lectin family, displays preferential binding to N-acetylgalactosamine compared with galactose. The structural basis for selective binding to N-acetylgalactosamine has been investigated. Regions of the carbohydrate-recognition domain of the receptor believed to be important in preferential binding to N-acetylgalactosamine have been inserted into the homologous carbohydrate-recognition domain of a mannose-binding protein mutant that was previously altered to bind galactose. Introduction of a single histidine residue corresponding to residue 256 of the hepatic asialoglycoprotein receptor was found to cause a 14-fold increase in the relative affinity for N-acetylgalactosamine compared with galactose. The relative ability of various acyl derivatives of galactosamine to compete for binding to this modified carbohydrate-recognition domain suggest that it is a good model for the natural N-acetylgalactosamine binding site of the asialoglycoprotein receptor. Crystallographic analysis of this mutant carbohydrate-recognition domain in complex with N-acetylgalactosamine reveals a direct interaction between the inserted histidine residue and the methyl group of the N-acetyl substituent of the sugar. Evidence for the role of the side chain at position 208 of the receptor in positioning this key histidine residue was obtained from structural analysis and mutagenesis experiments. The corresponding serine residue in the modified carbohydrate-recognition domain of mannose-binding protein forms a hydrogen bond to the imidazole side chain. When this serine residue is changed to valine, loss in selectivity for N-acetylgalactosamine is observed. The structure of this mutant reveals that the beta-branched valine side chain interacts directly with the histidine side chain, resulting in an altered imidazole ring orientation.


    Related Citations: 
    • Selective Sugar Binding to the Carbohydrate Recognition Domains of the Rat Hepatic and Macrophage Asialoglycoprotein Receptors
      Iobst, S.T., Drickamer, K.
      (1996) J Biol Chem 271: 6686
    • Structural Basis of Galactose Recognition by C-Type Animal Lectins
      Kolatkar, A.R., Weis, W.I.
      (1996) J Biol Chem 271: 6679

    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, California 94305, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MANNOSE-BINDING PROTEIN-A
1, 2, 3
154Rattus norvegicusMutation(s): 7 
Gene Names: Mbl1
Find proteins for P19999 (Rattus norvegicus)
Go to UniProtKB:  P19999
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NGA
Query on NGA

Download CCD File 
1, 2, 3
N-ACETYL-D-GALACTOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-JAJWTYFOSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
1, 2, 3
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
1, 3
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NGAKd:  200000   nM  PDBBind
NGAKd:  200000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.92α = 90
b = 84.53β = 104.49
c = 97.86γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-06-17
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance