3DSZ

Engineered human lipocalin 2 in complex with Y-DTPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.213 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

High-affinity recognition of lanthanide(III) chelate complexes by a reprogrammed human lipocalin 2

Kim, H.J.Eichinger, A.Skerra, A.

(2009) J Am Chem Soc 131: 3565-3576

  • DOI: 10.1021/ja806857r
  • Primary Citation of Related Structures:  
    3DSZ, 3DTQ

  • PubMed Abstract: 
  • Human lipocalin 2 (Lcn2), also known as neutrophil gelatinase-associated lipocalin (NGAL), which naturally scavenges bacterial ferric siderophores, has been engineered to specifically bind rare-earth and related metal ions as chelate complexes with [(R)-2-amino-3-(4-aminophenyl)propyl]-trans-(S,S)-cyclohexane-1,2-diaminepentaacetic acid (p-NH(2)-Bn-CHX-A''-DTPA) ...

    Human lipocalin 2 (Lcn2), also known as neutrophil gelatinase-associated lipocalin (NGAL), which naturally scavenges bacterial ferric siderophores, has been engineered to specifically bind rare-earth and related metal ions as chelate complexes with [(R)-2-amino-3-(4-aminophenyl)propyl]-trans-(S,S)-cyclohexane-1,2-diaminepentaacetic acid (p-NH(2)-Bn-CHX-A''-DTPA). To this end, 12 amino acid residues in the ligand pocket of Lcn2, which is formed by four loops at the open end of an eight-stranded beta-barrel, were subjected to targeted random mutagenesis, and from the resulting library, variants with binding activity for the Me x DTPA group were selected using the method of bacterial phage display. One promising candidate was further developed in several cycles of in vitro affinity maturation using partial random mutagenesis and selection (via phage display and/or Escherichia coli colony screening) under conditions of increasing stringency. As result, an Lcn2 variant was obtained that binds Y x DTPA with a dissociation constant as low as 400 pM. The Lcn2 variant specifically recognizes the artificial ligand, as exemplified in (competitive) ELISA and real-time surface plasmon resonance analyses. DTPA-complexed Y(3+), Tb(3+), Gd(3+), and Lu(3+) are most tightly bound, comprising metal ions whose isotopes are in common use for radiotherapy and imaging. All of the Lcn2 variants are stably folded and can be functionally produced in high yield in E. coli. X-ray crystallographic analyses show that the new ligand is well-accommodated in the central cavity of the engineered lipocalin, whose fold is largely preserved, but that the mode of binding differs from the one seen with the natural ligand Fe x enterobactin. This structural study reveals analogies but also differences with respect to previously described antibody-metal chelate complexes. Notably, the functionalized side chain of DTPA protrudes from the ligand pocket of the lipocalin in such a way that its conjugates (with other haptens, for example) are recognized too. With their small sizes and robust fold based on a single polypeptide chain, the engineered Lcn2 variants provide novel modules and/or fusion partners for radionuclide-chelate capturing strategies that bear promise for medical diagnostics and therapy.


    Organizational Affiliation

    Lehrstuhl für Biologische Chemie, Technische Universität München, Freising-Weihenstephan, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
engineered human lipocalin 2A, B186Homo sapiensMutation(s): 0 
Gene Names: LCN2variant Tb7.N9HNLNGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens)
Explore P80188 
Go to UniProtKB:  P80188
PHAROS:  P80188
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LIZ (Subject of Investigation/LOI)
Query on LIZ

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]N-{(1S,2S)-2-[bis(carboxymethyl)amino]cyclohexyl}-N-{(2R)-2-[bis(carboxymethyl)amino]-3-[4-({[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]carbamothioyl}amino)phenyl]propyl}glycine
C30 H45 N5 O13 S
ZDJITWBUQUCYMP-VJBWXMMDSA-N
 Ligand Interaction
YT3
Query on YT3

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]YTTRIUM (III) ION
Y
GRTBAGCGDOYUBE-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
LIZ PDBBind:  3DSZ Kd: 17.1 (nM) from 1 assay(s)
Binding MOAD:  3DSZ Kd: 17.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.213 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.35α = 90
b = 82.35β = 90
c = 115.128γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance