1LKE

ENGINEERED LIPOCALIN DIGA16 IN COMPLEX WITH DIGOXIGENIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural mechanism of specific ligand recognition by a lipocalin tailored for the complexation of digoxigenin.

Korndoerfer, I.P.Schlehuber, S.Skerra, A.

(2003) J Mol Biol 330: 385-396

  • DOI: 10.1016/s0022-2836(03)00573-4
  • Primary Citation of Related Structures:  
    1KXO, 1LKE, 1LNM

  • PubMed Abstract: 
  • DigA16 is an artificial digoxigenin-binding protein, which was derived from the bilin-binding protein, a lipocalin of Pieris brassicae, via reshaping of its natural ligand pocket. Here we report the crystal structures of DigA16 in the presence of eit ...

    DigA16 is an artificial digoxigenin-binding protein, which was derived from the bilin-binding protein, a lipocalin of Pieris brassicae, via reshaping of its natural ligand pocket. Here we report the crystal structures of DigA16 in the presence of either digoxigenin or digitoxigenin and for the apo-protein at resolutions below 1.9A. As a consequence of the altogether 17 amino acid substitutions within the binding site significant structural changes have occurred in the four loops that form the entrance to the ligand pocket on top of the structurally conserved beta-barrel framework. For example, one loop adopts a new alpha-helical backbone structure, which seems to be induced by few critical side-chain contacts. Digoxigenin becomes almost fully buried (by 95%) upon complexation, whereby specificity for the hydrophilic steroid is maintained through hydrogen-bonding networks and shape complementarity. The differential binding of the related steroid digitoxigenin is mainly governed by an internal histidine residue, whose side-chain undergoes significant induced fit. Among those amino acids that line the ligand pocket two tyrosine and one tryptophan residue provide the largest contacts. Interestingly, corresponding three side-chains are found with the same mutual orientation in the anti-digoxigenin antibody 26-10, even though the hapten orientation is quite different there and only 66% of the steroid surface is buried in the combining site. Hence, in the case of the engineered lipocalin DigA16 an example of convergent in vitro evolution is observed. Generally, the remarkable structural plasticity of the loop region and the role of polar residues in the binding site illustrate the potential of the lipocalin scaffold for the generation of specific receptor proteins towards a variety of ligands.


    Related Citations: 
    • A Novel Type of Receptor Protein, based on the Lipocalin Scaffold, with Specificity for Digoxigenin
      Schlehuber, S., Beste, G., Skerra, A.
      (2000) J Mol Biol 297: 1105
    • Small Antibody-like Proteins with Prescribed Ligand Specificities Derived from the Lipocalin Fold.
      Beste, G., Schmidt, F.S., Stibora, T., Skerra, A.
      (1999) Proc Natl Acad Sci U S A 96: 1898

    Organizational Affiliation

    Lehrstuhl für Biologische Chemie, Technische Universität München, An der Saatzucht 5, 85350, Freising-Weihenstephan, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DigA16A184Pieris brassicaeMutation(s): 21 
Find proteins for P09464 (Pieris brassicae)
Explore P09464 
Go to UniProtKB:  P09464
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DOG
Query on DOG

Download CCD File 
A
DIGOXIGENIN
C23 H34 O5
SHIBSTMRCDJXLN-KCZCNTNESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DOGKd:  30.200000762939453   nM  Binding MOAD
DOGKd :  30.200000762939453   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.052α = 90
b = 63.988β = 91.53
c = 39.452γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-17
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Refinement description