3LB2

Two-site competitive inhibition in dehaloperoxidase-hemoglobin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Internal binding of halogenated phenols in dehaloperoxidase-hemoglobin inhibits peroxidase function.

Thompson, M.K.Davis, M.F.de Serrano, V.Nicoletti, F.P.Howes, B.D.Smulevich, G.Franzen, S.

(2010) Biophys.J. 99: 1586-1595

  • DOI: 10.1016/j.bpj.2010.05.041
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Dehaloperoxidase (DHP) from the annelid Amphitrite ornata is a catalytically active hemoglobin-peroxidase that possesses a unique internal binding cavity in the distal pocket above the heme. The previously published crystal structure of DHP shows 4-i ...

    Dehaloperoxidase (DHP) from the annelid Amphitrite ornata is a catalytically active hemoglobin-peroxidase that possesses a unique internal binding cavity in the distal pocket above the heme. The previously published crystal structure of DHP shows 4-iodophenol bound internally. This led to the proposal that the internal binding site is the active site for phenol oxidation. However, the native substrate for DHP is 2,4,6-tribromophenol, and all attempts to bind 2,4,6-tribromophenol in the internal site under physiological conditions have failed. Herein, we show that the binding of 4-halophenols in the internal pocket inhibits enzymatic function. Furthermore, we demonstrate that DHP has a unique two-site competitive binding mechanism in which the internal and external binding sites communicate through two conformations of the distal histidine of the enzyme, resulting in nonclassical competitive inhibition. The same distal histidine conformations involved in DHP function regulate oxygen binding and release during transport and storage by hemoglobins and myoglobins. This work provides further support for the hypothesis that DHP possesses an external binding site for substrate oxidation, as is typical for the peroxidase family of enzymes.


    Organizational Affiliation

    Department of Chemistry, North Carolina State University, Raleigh, North Carolina, 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, 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
BML
Query on BML

Download SDF File 
Download CCD File 
A, B
4-BROMOPHENOL
C6 H5 Br O
GZFGOTFRPZRKDS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BMLKd: 1150000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.06 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.007α = 90.00
b = 67.358β = 90.00
c = 69.420γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
SCALEPACKdata scaling
DENZOdata reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance