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


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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 Glycosylation3D 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

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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

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H [auth A],
S [auth A],
U [auth A]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
GOL
Query on GOL

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R [auth A],
W [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
BR
Query on BR

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T [auth A]BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
OSM
Query on OSM

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I [auth A]
J [auth A]
K [auth A]
L [auth A]
M [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 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HEMClick on this verticalbar to view detailsBest fitted NAGClick on this verticalbar to view details

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