4IMO

Crystal structure of wild type human Lipocalin PGDS in complex with substrate analog U44069

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structural and dynamic insights into substrate binding and catalysis of human lipocalin prostaglandin D synthase.

Lim, S.M., Chen, D., Teo, H., Roos, A., Jansson, A.E., Nyman, T., Tresaugues, L., Pervushin, K., Nordlund, P.

(2013) J Lipid Res 54: 1630-1643

  • DOI: 10.1194/jlr.M035410
  • Primary Citation of Related Structures:  
    2WWP, 4IMN, 4IMO

  • PubMed Abstract: 

    • Lipocalin prostaglandin D synthase (L-PGDS) regulates synthesis of an important inflammatory and signaling mediator, prostaglandin D2 (PGD2). Here, we used structural, biophysical, and biochemical approaches to address the mechanistic aspects of substrat ...

    Lipocalin prostaglandin D synthase (L-PGDS) regulates synthesis of an important inflammatory and signaling mediator, prostaglandin D2 (PGD2). Here, we used structural, biophysical, and biochemical approaches to address the mechanistic aspects of substrate entry, catalysis, and product exit of this enzyme. Structure of human L-PGDS was solved in a complex with a substrate analog (SA) and in ligand-free form. Its catalytic Cys 65 thiol group was found in two different conformations, each making a distinct hydrogen bond network to neighboring residues. These help in elucidating the mechanism of the cysteine nucleophile activation. Electron density for ligand observed in the active site defined the substrate binding regions, but did not allow unambiguous fitting of the SA. To further understand ligand binding, we used NMR spectroscopy to map the binding sites and to show the dynamics of protein-substrate and protein-product interactions. A model for ligand binding at the catalytic site is proposed, showing a second binding site involved in ligand exit and entry. NMR chemical shift perturbations and NMR resonance line-width alterations (observed as changes of intensity in two-dimensional cross-peaks in [¹H,¹⁵N]-transfer relaxation optimization spectroscopy) for residues at the Ω loop (A-B loop), E-F loop, and G-H loop besides the catalytic sites indicate involvement of these residues in ligand entry/egress.

    Organizational Affiliation: 

    Division of Structural Biology and Biochemistry, Nanyang Technological University, Singapore.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipocalin-type prostaglandin-D synthase A176Homo sapiensMutation(s): 0 
Gene Names: PDS, PTGDS
EC: 5.3.99.2
Find proteins for P41222 (Homo sapiens)
Explore P41222 
Go to UniProtKB:  P41222
NIH Common Fund Data Resources
PHAROS:  P41222
GTEx:  ENSG00000107317
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PWZ
Query on PWZ
Download Ideal Coordinates CCD File 
A
(5E)-7-{(1R,4S,5S,6R)-5-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-2-oxabicyclo[2.2.1]hept-6-yl}hept-5-enoic acid
C21 H34 O4
DJKDIKIDYDXHDD-JVCJGEKZSA-N		 Ligand Interaction
SCN
Query on SCN
Download Ideal Coordinates CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.24α = 90
b = 56.38β = 90
c = 72.92γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references