5WV3 | pdb_00005wv3

Crystal structure of bovine lactoperoxidase with a partial Glu258-heme linkage at 2.07 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 
    0.236 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history

Literature

Structural basis of activation of mammalian heme peroxidases

Singh, P.K.Iqbal, N.Sirohi, H.V.Bairagya, H.R.Kaur, P.Sharma, S.Singh, T.P.

(2018) Prog Biophys Mol Biol 133: 49-55

  • DOI: https://doi.org/10.1016/j.pbiomolbio.2017.11.003
  • Primary Citation Related Structures: 
    5WV3

  • PubMed Abstract: 

    The mammalian heme peroxidases including lactoperoxidase (LPO), myeloperoxidase (MPO), eosinophil peroxidase (EPO) and thyroid peroxidase (TPO) contain a covalently linked heme moiety. Initially, it was believed that the heme group was fully cross-linked to protein molecule through at least two ester linkages involving conserved glutamate and aspartate residues with 1-methyl and 5-methyl groups of pyrrole rings A and C respectively. In MPO, an additional sulfonium ion linkage was present between 2-vinyl group of pyrrole ring A of the heme moiety and a methionine residue of the protein. These linkages were formed through a self processing mechanism. Subsequently, biochemical studies indicated that the heme moiety was partially attached to protein. The recent structural studies have shown that the covalent linkage involving glutamate and 1-methyl group of pyrrole ring of heme moiety was partially formed. When glutamate is not covalently linked to heme moiety, its side chain occupies a position in the substrate binding site on the distal heme side and blocks the substrate binding site leading to inactivation. However, an exposure to H 2 O 2 converts it to a fully covalently linked state with heme. Thus in mammalian heme peroxidases, the Glu-heme linkage is essential for catalytic action.


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

Macromolecule Content 

  • Total Structure Weight: 71.02 kDa 
  • Atom Count: 5,214 
  • 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
Lactoperoxidase595Bos taurusMutation(s): 0 
EC: 1.11.1.7
UniProt
Find proteins for P80025 (Bos taurus)
Explore P80025 
Go to UniProtKB:  P80025
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80025
Glycosylation
Glycosylation Sites: 4
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
D [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NAG

Query on NAG



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
H [auth A],
S [auth A],
U [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL

Query on GOL



Download:Ideal Coordinates CCD File
R [auth A],
W [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR

Query on BR



Download:Ideal Coordinates CCD File
T [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
OSM

Query on OSM



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [auth A]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
V [auth A]
1-(OXIDOSULFANYL)METHANAMINE
C H5 N O S
KONFWJXIYYGXOO-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.012α = 90
b = 79.809β = 93.01
c = 66.106γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-03-08
    Changes: Other
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.3: 2018-07-18
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.0: 2025-03-12
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary