1EW6

THE CRYSTAL STRUCTURE AND AMINO ACID SEQUENCE OF DEHALOPEROXIDASE FROM AMPHITRITE ORNATA INDICATE COMMON ANCESTRY WITH GLOBINS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The crystal structure and amino acid sequence of dehaloperoxidase from Amphitrite ornata indicate common ancestry with globins.

LaCount, M.W.Zhang, E.Chen, Y.P.Han, K.Whitton, M.M.Lincoln, D.E.Woodin, S.A.Lebioda, L.

(2000) J Biol Chem 275: 18712-18716

  • DOI: 10.1074/jbc.M001194200
  • Primary Citation of Related Structures:  
    1EW6, 1EWA

  • PubMed Abstract: 
  • The full-length, protein coding sequence for dehaloperoxidase was obtained using a reverse genetic approach and a cDNA library from marine worm Amphitrite ornata. The crystal structure of the dehaloperoxidase (DHP) was determined by the multiple isom ...

    The full-length, protein coding sequence for dehaloperoxidase was obtained using a reverse genetic approach and a cDNA library from marine worm Amphitrite ornata. The crystal structure of the dehaloperoxidase (DHP) was determined by the multiple isomorphous replacement method and was refined at 1.8-A resolution. The enzyme fold is that of the globin family and, together with the amino acid sequence information, indicates that the enzyme evolved from an ancient oxygen carrier. The peroxidase activity of DHP arose mainly through changes in the positions of the proximal and distal histidines relative to those seen in globins. The structure of a complex of DHP with 4-iodophenol is also reported, and it shows that in contrast to larger heme peroxidases DHP binds organic substrates in the distal cavity. The binding is facilitated by the histidine swinging in and out of the cavity. The modeled position of the oxygen atom bound to the heme suggests that the enzymatic reaction proceeds via direct attack of the oxygen atom on the carbon atom bound to the halogen atom.


    Organizational Affiliation

    Departments of Chemistry and Biochemistry and Biological Sciences, University of South Carolina, Columbia, South Carolina 29208, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DEHALOPEROXIDASEA, B137Amphitrite ornataMutation(s): 0 
Find proteins for Q9NAV8 (Amphitrite ornata)
Explore Q9NAV8 
Go to UniProtKB:  Q9NAV8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.5α = 90
b = 68.4β = 90
c = 61γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2000-04-24 
  • Released Date: 2000-05-10 
  • Deposition Author(s): Lebioda, L.

Revision History 

  • Version 1.0: 2000-05-10
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance