1RIR

Crystal structure of meso-tetrasulphonatophenylporphyrin in complex with Peanut lectin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of the PNA-porphyrin complex in the presence and absence of lactose: mapping the conformational changes on lactose binding, interacting surfaces, and supramolecular aggregations.

Goel, M.Damai, R.S.Sethi, D.K.Kaur, K.J.Maiya, B.G.Swamy, M.J.Salunke, D.M.

(2005) Biochemistry 44: 5588-5596

  • DOI: 10.1021/bi047377s
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The extraordinary recognition specificity of lectins for carbohydrate ligands appears to be violated as they also bind to porphyrins and other noncarbohydrate ligands. In this study, crystal structures of meso-tetrasulfonatophenylporphyrin (H(2)TPPS) ...

    The extraordinary recognition specificity of lectins for carbohydrate ligands appears to be violated as they also bind to porphyrins and other noncarbohydrate ligands. In this study, crystal structures of meso-tetrasulfonatophenylporphyrin (H(2)TPPS) bound to peanut agglutinin (PNA) in the presence and absence of lactose were determined. The binding of H(2)TPPS with PNA involved 11 molecules of H(2)TPPS in different supramolecular stacking arrangements associated with a tetramer of PNA in the crystals of the PNA-H(2)TPPS binary complex as well as the PNA-H(2)TPPS-lactose ternary complex. The ternary complex involved lactose binding only to two subunits of the PNA tetramer, which did not have porphyrin interacting in the vicinity of the carbohydrate-binding site. Comparison of the two structures highlighted the plasticity of the carbohydrate-binding site expressed in terms of the conformational change in lactose binding. The unusual quaternary structure of PNA, which results in exposed protein-protein interaction sites, might be responsible for the porphyrin binding. The association of porphyrin in diverse oligomeric stacking arrangements observed in the PNA-H(2)TPPS complex suggested the possibility of protein-porphyrin aggregation under abnormal physiological conditions. The structures described here provide a possible native conformation of the carbohydrate-binding site of PNA in the absence of the ligand, highlight mapping of the unsaturated binding surfaces of PNA using porphyrin interactions, indicate new leads toward possible application of this lectin in photodynamic therapy, and exhibit diverse modes of porphyrin-lectin interactions with implications to porphyria, a disease that results from abnormal accumulation of porphyrins.


    Related Citations: 
    • Functional equality in the absence of structural similarity: an added dimension to molecular mimicry.
      Goel, M.,Jain, D.,Kaur, K.J.,Kenoth, R.,Maiya, B.G.,Swamy, M.J.,Salunke, D.M.
      (2001) J.Biol.Chem. 276: 39277


    Organizational Affiliation

    National Institute of Immunology, New Delhi 110067, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Galactose-binding lectin
A, B, C, D
236Arachis hypogaeaMutation(s): 0 
Find proteins for P02872 (Arachis hypogaea)
Go to UniProtKB:  P02872
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SFP
Query on SFP

Download SDF File 
Download CCD File 
A, B, C, D
5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE
C44 H34 N4 O12 S4
OVPFWIRROXFHGQ-LWQDQPMZSA-J
 Ligand Interaction
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.234 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 94.800α = 90.00
b = 94.800β = 90.00
c = 144.000γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance