4QYQ

Crystal structure of the complex of goat lactoperoxidase with an antithyroid agent propylthiouracil at 2.5 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mode of binding of the antithyroid drug propylthiouracil to mammalian haem peroxidases

Singh, R.P.Singh, A.Kushwaha, G.S.Singh, A.K.Kaur, P.Sharma, S.Singh, T.P.

(2015) Acta Crystallogr.,Sect.F 71: 304-310

  • DOI: 10.1107/S2053230X15001806
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mammalian haem peroxidase superfamily consists of myeloperoxidase (MPO), lactoperoxidase (LPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO). These enzymes catalyze a number of oxidative reactions of inorganic substrates such as Cl(-) ...

    The mammalian haem peroxidase superfamily consists of myeloperoxidase (MPO), lactoperoxidase (LPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO). These enzymes catalyze a number of oxidative reactions of inorganic substrates such as Cl(-), Br(-), I(-) and SCN(-) as well as of various organic aromatic compounds. To date, only structures of MPO and LPO are known. The substrate-binding sites in these enzymes are located on the distal haem side. Propylthiouracil (PTU) is a potent antithyroid drug that acts by inhibiting the function of TPO. It has also been shown to inhibit the action of LPO. However, its mode of binding to mammalian haem peroxidases is not yet known. In order to determine the mode of its binding to peroxidases, the structure of the complex of LPO with PTU has been determined. It showed that PTU binds to LPO in the substrate-binding site on the distal haem side. The IC50 values for the inhibition of LPO and TPO by PTU are 47 and 30 µM, respectively. A comparision of the residues surrounding the substrate-binding site on the distal haem side in LPO with those in TPO showed that all of the residues were identical except for Ala114 (LPO numbering scheme), which is replaced by Thr205 (TPO numbering scheme) in TPO. A threonine residue in place of alanine in the substrate-binding site may affect the affinity of PTU for peroxidases.


    Organizational Affiliation

    Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lactoperoxidase
A, B, C, D
595Capra hircusMutation(s): 0 
Gene Names: LPO
Find proteins for A3F9D6 (Capra hircus)
Go to Gene View: LPO
Go to UniProtKB:  A3F9D6
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
3CJ
Query on 3CJ

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Download CCD File 
A, B, C, D
6-propyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one
C7 H10 N2 O S
KNAHARQHSZJURB-UHFFFAOYSA-N
 Ligand Interaction
NO3
Query on NO3

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Download CCD File 
A, B, C, D
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.245 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 80.221α = 80.91
b = 82.588β = 73.71
c = 95.083γ = 89.96
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
HKL-2000data reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2015-04-01
    Type: Database references