1BYF

STRUCTURE OF TC14; A C-TYPE LECTIN FROM THE TUNICATE POLYANDROCARPA MISAKIENSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of a tunicate C-type lectin from Polyandrocarpa misakiensis complexed with D -galactose.

Poget, S.F.Legge, G.B.Proctor, M.R.Butler, P.J.Bycroft, M.Williams, R.L.

(1999) J.Mol.Biol. 290: 867-879

  • DOI: 10.1006/jmbi.1999.2910
  • Primary Citation of Related Structures:  1TLG

  • PubMed Abstract: 
  • C-type lectins are calcium-dependent carbohydrate-recognising proteins. Isothermal titration calorimetry of the C-type Polyandrocarpa lectin (TC14) from the tunicate Polyandrocarpa misakiensis revealed the presence of a single calcium atom per monome ...

    C-type lectins are calcium-dependent carbohydrate-recognising proteins. Isothermal titration calorimetry of the C-type Polyandrocarpa lectin (TC14) from the tunicate Polyandrocarpa misakiensis revealed the presence of a single calcium atom per monomer with a dissociation constant of 2.6 microM, and confirmed the specificity of TC14 for D -galactose and related monosaccharides. We have determined the 2.2 A X-ray crystal structure of Polyandrocarpa lectin complexed with D -galactose. Analytical ultracentrifugation revealed that TC14 behaves as a dimer in solution. This is reflected by the presence of two molecules in the asymmetric unit with the dimeric interface formed by antiparallel pairing of the two N-terminal beta-strands and hydrophobic interactions. TC14 adopts a typical C-type lectin fold with differences in structure from other C-type lectins mainly in the diverse loop regions and in the second alpha-helix, which is involved in the formation of the dimeric interface. The D -galactose is bound through coordination of the 3 and 4-hydroxyl oxygen atoms with a bound calcium atom. Additional hydrogen bonds are formed directly between serine, aspartate and glutamate side-chains of the protein and the sugar 3 and 4-hydroxyl groups. Comparison of the galactose binding by TC14 with the mannose binding by rat mannose-binding protein reveals how monosaccharide specificity is achieved in this lectin. A tryptophan side-chain close to the binding site and the distribution of hydrogen-bond acceptors and donors around the 3 and 4-hydroxyl groups of the sugar are essential determinants of specificity. These elements are, however, arranged in a very different way than in an engineered galactose-specific mutant of MBPA. Possible biological functions can more easily be understood from the fact that TC14 is a dimer under physiological conditions.


    Related Citations: 
    • A Calcium-Dependent Galactose-Binding Lectin from the Tunicate Polyandrocarpa Misakiensis. Isolation, Characterization, and Amino Acid Sequence
      Suzuki, T.,Takagi, T.,Furukohri, T.,Kawamura, K.,Nakauchi, M.
      (1990) J.Biol.Chem. 265: 1274
    • Expression of Genes for 2 C-Type Lectins During Budding of the Ascidian Polyandrocarpa-Misakiensis
      Shimada, M.,Fujiwara, S.,Kawamura, K.
      (1995) Roux's Arch.Dev.Biol. 204: 406
    • Budding-Specific Lectin Induced in Epithelial Cells is an Extracellular Matrix Component for Stem Cell Aggregation in Tunicates
      Kawamura, K.,Fujiwara, S.,Sugino, Y.M.
      (1991) DEVELOPMENT 113: 995


    Organizational Affiliation

    Cambridge Centre for Protein Engineering, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK. sfp22@cam.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (POLYANDROCARPA LECTIN)
A, B
125Polyandrocarpa misakiensisN/A
Find proteins for P16108 (Polyandrocarpa misakiensis)
Go to UniProtKB:  P16108
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.180α = 90.00
b = 66.450β = 90.00
c = 85.900γ = 90.00
Software Package:
Software NamePurpose
SHARPphasing
REFMACrefinement
CCP4data scaling
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-23
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance