7VE3 | pdb_00007ve3

Structure of the complex of sheep lactoperoxidase with hypoiodite at 2.70 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.277 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.195 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural evidence of the oxidation of iodide ion into hyper-reactive hypoiodite ion by mammalian heme lactoperoxidase.

Singh, P.K.Ahmad, N.Yamini, S.Singh, R.P.Singh, A.K.Sharma, P.Smith, M.L.Sharma, S.Singh, T.P.

(2022) Protein Sci 31: 384-395

  • DOI: https://doi.org/10.1002/pro.4230
  • Primary Citation Related Structures: 
    7VE3

  • PubMed Abstract: 

    Lactoperoxidase (1.11.1.7, LPO) is a mammalian heme peroxidase found in the extracellular fluids of mammals including plasma, saliva, airway epithelial lining fluids, nasal lining fluid, milk, tears, gastric juices, and intestinal mucosa. To perform its innate immune action against invading microbes, LPO utilizes hydrogen peroxide (H 2 O 2 ) to convert thiocyanate (SCN - ) and iodide (I - ) ions into the oxidizing compounds hypothiocyanite (OSCN - ) and hypoiodite (IO - ). Previously determined structures of the complexes of LPO with SCN - , OSCN - , and I - show that SCN - and I - occupy appropriate positions in the distal heme cavity as substrates while OSCN - binds in the distal heme cavity as a product inhibitor. We report here the structure of the complex of LPO with IO - as the first structural evidence of the conversion of iodide into hypoiodite by LPO. To obtain this complex, a solution of LPO was first incubated with H 2 O 2 , then mixed with ammonium iodide solution and the complex crystallized by the addition of PEG-3350, 20% (wt/vol). These crystals were used for X-ray intensity data collection and structure analysis. The structure determination revealed the presence of four hypoiodite ions in the substrate binding channel of LPO. In addition to these, six other hypoiodite ions were observed at different exterior sites. We surmise that the presence of hypoiodite ions in the distal heme cavity blocks the substrate binding site and inhibits catalysis. This was confirmed by activity experiments with the colorimetric substrate, ABTS (2,2'-azino-bis(3-ethylbenzthiazoline-sulfonic acid)), in the presence of hypoiodite and iodide ions.


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

Macromolecule Content 

  • Total Structure Weight: 71.24 kDa 
  • Atom Count: 5,031 
  • Modeled Residue Count: 595 
  • Deposited Residue Count: 595 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lactoperoxidase595Ovis ariesMutation(s): 0 
EC: 1.11.1.7

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
61D
(Subject of Investigation/LOI)

Query on 61D



Download:Ideal Coordinates CCD File
M [auth A]
N [auth A]
O [auth A]
P [auth A]
Q [auth A]
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A]
hypoiodous acid
H I O
GEOVEUCEIQCBKH-UHFFFAOYSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4

Query on SO4



Download:Ideal Coordinates CCD File
L [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.277 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.942α = 90
b = 80.179β = 102.86
c = 76.122γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references
  • Version 1.2: 2022-02-23
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2025-09-17
    Changes: Derived calculations, Structure summary