1CL6

CRYSTAL STRUCTURES OF FERRIC-NO COMPLEXES OF FUNGAL NITRIC OXIDE REDUCTASE AND ITS SER286 MUTANTS AT CRYOGENIC TEMPERATURE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Proton delivery in NO reduction by fungal nitric-oxide reductase. Cryogenic crystallography, spectroscopy, and kinetics of ferric-NO complexes of wild-type and mutant enzymes.

Shimizu, H.Obayashi, E.Gomi, Y.Arakawa, H.Park, S.Y.Nakamura, H.Adachi, S.Shoun, H.Shiro, Y.

(2000) J.Biol.Chem. 275: 4816-4826

  • Primary Citation of Related Structures:  1CMJ, 1CMN

  • PubMed Abstract: 
  • Fungal nitric-oxide reductase (NOR) is a heme enzyme that catalyzes the reduction of NO to N(2)O through its ferric-NO complex, the first intermediate of the catalysis. Crystal structures of the ferric-NO forms of wild type (WT) fungal NOR, and of th ...

    Fungal nitric-oxide reductase (NOR) is a heme enzyme that catalyzes the reduction of NO to N(2)O through its ferric-NO complex, the first intermediate of the catalysis. Crystal structures of the ferric-NO forms of wild type (WT) fungal NOR, and of the Ser(286) --> Val and Ser(286) --> Thr mutant enzymes were determined to 1.7-A resolution at cryogenic temperature (100 K). This shows a slightly tilted and bent NO binding to the heme iron, in sharp contrast to the highly bent NO coordination found in ferrous hemoproteins. In the WT structure, a specific hydrogen-bonding network that connects the active site to the solvent was identified, H(2)O(Wat(74))-Ser(286)-H(2)O(Wat(33))-Asp(393)-solvent. Wat(74) is located 3.10 A from the iron-bound NO. Replacement of Ser(286) with Val or Thr scarcely alters the NO coordination structure but expels the water molecules, Wat(74) from the active site. The Asp(393) mutation does not influence the position of Wat(74), but disrupts the hydrogen-bonding network at Wat(33), as evidenced by enzymatic, kinetic, and spectroscopic (resonance Raman and IR) results. The structural changes observed upon the Ser(286) or the Asp(393) mutation are consistent with the dramatic loss of the enzymatic activity for the NO reduction of fungal NOR. We have conclusively identified the water molecule, Wat(74), adjacent to the iron-bound NO as a proton donor to the Fe-NO moiety. In addition, we find the hydrogen-bonding network, H(2)O(Wat(74))-Ser(286)-H(2)O(Wat(33))-Asp(393), as a proton delivery pathway in the NO reduction reaction by fungal NOR.


    Organizational Affiliation

    The Faculty of Science, Gakushuin University, Mejiro, Toshima-ku, Tokyo 170-0031, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOCHROME P450
A
402Fusarium oxysporumGene Names: CYP55A1 (CYP55)
EC: 1.7.1.14
Find proteins for P23295 (Fusarium oxysporum)
Go to UniProtKB:  P23295
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NO
Query on NO

Download SDF File 
Download CCD File 
A
NITRIC OXIDE
Nitrogen monoxide
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.530α = 90.00
b = 81.710β = 90.00
c = 85.550γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORrefinement
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-05-06 
  • Released Date: 2000-03-22 
  • Deposition Author(s): Park, S.-Y., Shiro, Y.

Revision History 

  • Version 1.0: 2000-03-22
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance