3FW4

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric Catechol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Iron traffics in circulation bound to a siderocalin (Ngal)-catechol complex.

Bao, G.Clifton, M.Hoette, T.M.Mori, K.Deng, S.X.Qiu, A.Viltard, M.Williams, D.Paragas, N.Leete, T.Kulkarni, R.Li, X.Lee, B.Kalandadze, A.Ratner, A.J.Pizarro, J.C.Schmidt-Ott, K.M.Landry, D.W.Raymond, K.N.Strong, R.K.Barasch, J.

(2010) Nat Chem Biol 6: 602-609

  • DOI: 10.1038/nchembio.402
  • Primary Citation of Related Structures:  
    3FW4, 3FW5

  • PubMed Abstract: 
  • The lipocalins are secreted proteins that bind small organic molecules. Scn-Ngal (also known as neutrophil gelatinase associated lipocalin, siderocalin, lipocalin 2) sequesters bacterial iron chelators, called siderophores, and consequently blocks bacterial growth ...

    The lipocalins are secreted proteins that bind small organic molecules. Scn-Ngal (also known as neutrophil gelatinase associated lipocalin, siderocalin, lipocalin 2) sequesters bacterial iron chelators, called siderophores, and consequently blocks bacterial growth. However, Scn-Ngal is also prominently expressed in aseptic diseases, implying that it binds additional ligands and serves additional functions. Using chemical screens, crystallography and fluorescence methods, we report that Scn-Ngal binds iron together with a small metabolic product called catechol. The formation of the complex blocked the reactivity of iron and permitted its transport once introduced into circulation in vivo. Scn-Ngal then recycled its iron in endosomes by a pH-sensitive mechanism. As catechols derive from bacterial and mammalian metabolism of dietary compounds, the Scn-Ngal-catechol-Fe(III) complex represents an unforeseen microbial-host interaction, which mimics Scn-Ngal-siderophore interactions but instead traffics iron in aseptic tissues. These results identify an endogenous siderophore, which may link the disparate roles of Scn-Ngal in different diseases.


    Organizational Affiliation

    College of Physicians and Surgeons of Columbia University, New York, New York, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neutrophil gelatinase-associated lipocalinA, B, C178Homo sapiensMutation(s): 1 
Gene Names: HNLLCN2NGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens)
Explore P80188 
Go to UniProtKB:  P80188
PHAROS:  P80188
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAQ
Query on CAQ

Download Ideal Coordinates CCD File 
E [auth A], T [auth C]CATECHOL
C6 H6 O2
YCIMNLLNPGFGHC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth C] , BA [auth C] , CA [auth C] , DA [auth C] , EA [auth C] , FA [auth C] , I [auth A] , J [auth A] , 
AA [auth C],  BA [auth C],  CA [auth C],  DA [auth C],  EA [auth C],  FA [auth C],  I [auth A],  J [auth A],  K [auth A],  Y [auth C],  Z [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
D [auth A], P [auth B], S [auth C]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
GA [auth C], H [auth A], L [auth A], M [auth A], N [auth A], O [auth A], Q [auth B], R [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A], G [auth A], U [auth C], V [auth C], W [auth C], X [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CAQKd :  0.4000000059604645   nM  PDBBind
CAQKd:  0.4000000059604645   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.256 
  • R-Value Observed: 0.258 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.421α = 90
b = 115.421β = 90
c = 118.801γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance