4MEC

Crystal structure of RAT Heme oxygenase-1 in complex with ZN(II)-Protoporphyrin IX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.249 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Distal regulation of heme binding of heme oxygenase-1 mediated by conformational fluctuations

Harada, E.Sugishima, M.Harada, J.Fukuyama, K.Sugase, K.

(2015) Biochemistry 54: 340-348

  • DOI: 10.1021/bi5009694

  • PubMed Abstract: 
  • Heme oxygenase-1 (HO-1) is an enzyme that catalyzes the oxidative degradation of heme. Since free heme is toxic to cells, rapid degradation of heme is important for maintaining cellular health. There have been useful mechanistic studies of the HO rea ...

    Heme oxygenase-1 (HO-1) is an enzyme that catalyzes the oxidative degradation of heme. Since free heme is toxic to cells, rapid degradation of heme is important for maintaining cellular health. There have been useful mechanistic studies of the HO reaction based on crystal structures; however, how HO-1 recognizes heme is not completely understood because the crystal structure of heme-free rat HO-1 lacks electron densities for A-helix that ligates heme. In this study, we characterized conformational dynamics of HO-1 using NMR to elucidate the mechanism by which HO-1 recognizes heme. NMR relaxation experiments showed that the heme-binding site in heme-free HO-1 fluctuates in concert with a surface-exposed loop and transiently forms a partially unfolded structure. Because the fluctuating loop is located over 17 Å distal from the heme-binding site and its conformation is nearly identical among different crystal structures including catalytic intermediate states, the function of the loop has been unexamined. In the course of elucidating its function, we found interesting mutations in this loop that altered activity but caused little change to the conformation. The Phe79Ala mutation in the loop changed the conformational dynamics of the heme-binding site. Furthermore, the heme binding kinetics of the mutant was slower than that of the wild type. Hence, we concluded that the distal loop is involved in the regulation of the conformational change for heme binding through the conformational fluctuations. Similar to other enzymes, HO-1 effectively promotes its function using the identified distal sites, which might be potential targets for protein engineering.


    Organizational Affiliation

    Bioorganic Research Institute, Suntory Foundation for Life Sciences , 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heme oxygenase 1
A, B, C, D, E, F, G
232Rattus norvegicusGene Names: Hmox1
EC: 1.14.14.18
Find proteins for P06762 (Rattus norvegicus)
Go to UniProtKB:  P06762
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZNH
Query on ZNH

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
PROTOPORPHYRIN IX CONTAINING ZN
C34 H32 N4 O4 Zn
FUTVBRXUIKZACV-UMRYFLQFDI
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.249 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.059α = 86.41
b = 73.167β = 87.62
c = 148.757γ = 86.25
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-08-26 
  • Released Date: 2014-08-27 
  • Deposition Author(s): Sugishima, M.

Revision History 

  • Version 1.0: 2014-08-27
    Type: Initial release
  • Version 1.1: 2016-06-01
    Type: Database references