1P3T

Crystal Structures of the NO-and CO-Bound Heme Oxygenase From Neisseria Meningitidis: Implications for Oxygen Activation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.254 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structures of the NO- and CO-bound heme oxygenase from Neisseriae meningitidis. Implications for O2 activation

Friedman, J.Lad, L.Deshmukh, R.Li, H.Wilks, A.Poulos, T.L.

(2003) J Biol Chem 278: 34654-34659

  • DOI: 10.1074/jbc.M302985200
  • Primary Citation of Related Structures:  
    1P3T, 1P3U, 1P3V

  • PubMed Abstract: 
  • Heme oxygenases catalyze the oxidation of heme to biliverdin, carbon monoxide, and free iron while playing a critical role in mammalian heme homeostasis. Pathogenic bacteria such as Neisseriae meningitidis also produce heme oxygenase as part of a mechanism to mine host iron ...

    Heme oxygenases catalyze the oxidation of heme to biliverdin, carbon monoxide, and free iron while playing a critical role in mammalian heme homeostasis. Pathogenic bacteria such as Neisseriae meningitidis also produce heme oxygenase as part of a mechanism to mine host iron. The key step in heme oxidation is the regioselective oxidation of the heme alpha-meso-carbon by an activated Fe(III)-OOH complex. The structures of various diatomic ligands bound to the heme iron can mimic the dioxygen complex and provide important insights on the mechanism of O2 activation. Here we report the crystal structures of N. meningitidis heme oxygenase (nm-HO) in the Fe(II), Fe(II)-CO, and Fe(II)-NO states and compare these to the NO complex of human heme oxygenase-1 (Lad, L., Wang, J., Li, H., Friedman, J., Bhaskar, B., Ortiz de Montellano, P. R., and Poulos, T. L. (2003) J. Mol. Biol. 330, 527-538). Coordination of NO or CO results in a reorientation of Arg-77 that enables Arg-77 to participate in an active site H-bonded network involving a series of water molecules. One of these water molecules directly H-bonds to the Fe(II)-linked ligand and very likely serves as the proton source required for oxygen activation. Although the active site residues differ between nm-HO and human HO-1, the close similarity in the H-bonded water network suggests a common mechanism shared by all heme oxygenases.


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, and Program in Macromolecular Structure, University of California, Irvine, California 92697, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Heme oxygenase 1A209Neisseria meningitidisMutation(s): 0 
Gene Names: hemONMA510612_2169
EC: 1.14.99.3
UniProt
Find proteins for Q9RGD9 (Neisseria meningitidis)
Explore Q9RGD9 
Go to UniProtKB:  Q9RGD9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RGD9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.254 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.245α = 90
b = 63.245β = 90
c = 102.142γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance