3DR9

Increased Distal Histidine Conformational Flexibility in the Deoxy Form of Dehaloperoxidase from Amphitrite ornata


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Distal histidine conformational flexibility in dehaloperoxidase from Amphitrite ornata.

Chen, Z.de Serrano, V.Betts, L.Franzen, S.

(2009) Acta Crystallogr.,Sect.D 65: 34-40

  • DOI: 10.1107/S0907444908036548

  • PubMed Abstract: 
  • The enzyme dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a heme protein which has a globin fold but can function as both a hemoglobin and a peroxidase. As a peroxidase, DHP is capable of converting 2,4,6-trihalophenols to ...

    The enzyme dehaloperoxidase (DHP) from the terebellid polychaete Amphitrite ornata is a heme protein which has a globin fold but can function as both a hemoglobin and a peroxidase. As a peroxidase, DHP is capable of converting 2,4,6-trihalophenols to the corresponding 2,6-dihaloquinones in the presence of hydrogen peroxide. As a hemoglobin, DHP cycles between the oxy and deoxy states as it reversibly binds oxygen for storage. Here, it is reported that the distal histidine, His55, exhibits conformational flexibility in the deoxy form and is consequently observed in two solvent-exposed conformations more than 9.5 A away from the heme. These conformations are analogous to the open conformation of sperm whale myoglobin. The heme iron in deoxy ferrous DHP is five-coordinate and has an out-of-plane displacement of 0.25 A from the heme plane. The observation of five-coordinate heme iron with His55 in a remote solvent-exposed conformation is consistent with the hypothesis that His55 interacts with heme iron ligands through hydrogen bonding in the closed conformation. Since His55 is also displaced by the binding of 4-iodophenol in an internal pocket, these results provide new insight into the correlation between heme iron ligation, molecular binding in the distal pocket and the conformation of the distal histidine in DHP.


    Organizational Affiliation

    Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dehaloperoxidase A
A, B
137Amphitrite ornataMutation(s): 0 
Find proteins for Q9NAV8 (Amphitrite ornata)
Go to UniProtKB:  Q9NAV8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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: 1.26 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.517α = 90.00
b = 67.194β = 90.00
c = 69.094γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description