4KJT

Structure of the L100F MUTANT OF DEHALOPEROXIDASE-HEMOGLOBIN A FROM AMPHITRITE ORNATA WITH OXYGEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.133 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Influence of heme environment structure on dioxygen affinity for the dual function Amphitrite ornata hemoglobin/dehaloperoxidase. Insights into the evolutional structure-function adaptations.

Sun, S.Sono, M.Wang, C.Du, J.Lebioda, L.Dawson, J.H.

(2014) Arch.Biochem.Biophys. 545: 108-115

  • DOI: 10.1016/j.abb.2014.01.010

  • PubMed Abstract: 
  • Sea worm, Amphitrite ornata, has evolved its globin (an O(2) carrier) also to serves as a dehaloperoxidase (DHP) to detoxify haloaromatic pollutants generated by competing species. A previous mutagenesis study by our groups on both DHP and sperm whal ...

    Sea worm, Amphitrite ornata, has evolved its globin (an O(2) carrier) also to serves as a dehaloperoxidase (DHP) to detoxify haloaromatic pollutants generated by competing species. A previous mutagenesis study by our groups on both DHP and sperm whale myoglobin (SW Mb) revealed some structural factors that influence the dehaloperoxidase activities (significantly lower for Mb) of both proteins. Using an isocyanide/O(2) partition constant measurement method in this study, we have examined the effects of these structural factors on the O(2) equilibrium constants (KO2) of DHP, SW Mb, and their mutants. A clear trend of decreasing O(2) affinity and increasing catalytic activity along with the increase in the distal His N(ε)-heme iron distance is observed. An H93K/T95H Mb double mutant mimicking the DHP proximal His positioning exhibited markedly enhanced O(2) affinity, confirming the essential effect of proximal His rotation on the globin function of DHP. For DHP, the L100F, T56G and M86E variants showed the effects of distal volume, distal His flexibility and proximal electronic push, respectively, on the O(2) affinity. This study provides insights into how DHP has evolved its heme environment to gain significantly enhanced peroxidase capability without compromising its primary function as an O(2) carrier.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dehaloperoxidase A
A, B
137Amphitrite ornataMutation(s): 1 
Find proteins for Q9NAV8 (Amphitrite ornata)
Go to UniProtKB:  Q9NAV8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.133 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 59.128α = 90.00
b = 67.782β = 90.00
c = 68.132γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SERGUIdata collection
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description