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: 1.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.203 

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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

  • DOI: 10.1074/jbc.275.7.4816
  • Primary Citation of Related Structures:  
    1CL6, 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 the Ser(286) --> Val and Ser(286) --> Thr mutant enzymes were determined to 1 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOCHROME P450A402Fusarium oxysporumMutation(s): 0 
Gene Names: CYP55A1CYP55
EC: 1.14 (PDB Primary Data), 1.7.1.14 (UniProt)
UniProt
Find proteins for P23295 (Fusarium oxysporum)
Explore P23295 
Go to UniProtKB:  P23295
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
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
NO
Query on NO

Download Ideal Coordinates CCD File 
C [auth A]NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYAM
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.53α = 90
b = 81.71β = 90
c = 85.55γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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