7DVO

Structure of Reaction Intermediate of Cytochrome P450 NO Reductase (P450nor) Determined by XFEL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Short-lived intermediate in N 2 O generation by P450 NO reductase captured by time-resolved IR spectroscopy and XFEL crystallography.

Nomura, T.Kimura, T.Kanematsu, Y.Yamada, D.Yamashita, K.Hirata, K.Ueno, G.Murakami, H.Hisano, T.Yamagiwa, R.Takeda, H.Gopalasingam, C.Kousaka, R.Yanagisawa, S.Shoji, O.Kumasaka, T.Yamamoto, M.Takano, Y.Sugimoto, H.Tosha, T.Kubo, M.Shiro, Y.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2101481118
  • Primary Citation of Related Structures:  
    7DVO

  • PubMed Abstract: 

    Nitric oxide (NO) reductase from the fungus Fusarium oxysporum is a P450-type enzyme (P450nor) that catalyzes the reduction of NO to nitrous oxide (N 2 O) in the global nitrogen cycle. In this enzymatic reaction, the heme-bound NO is activated by the direct hydride transfer from NADH to generate a short-lived intermediate ( I ), a key state to promote N-N bond formation and N-O bond cleavage. This study applied time-resolved (TR) techniques in conjunction with photolabile-caged NO to gain direct experimental results for the characterization of the coordination and electronic structures of I TR freeze-trap crystallography using an X-ray free electron laser (XFEL) reveals highly bent Fe-NO coordination in I , with an elongated Fe-NO bond length (Fe-NO = 1.91 Å, Fe-N-O = 138°) in the absence of NAD + TR-infrared (IR) spectroscopy detects the formation of I with an N-O stretching frequency of 1,290 cm -1 upon hydride transfer from NADH to the Fe 3+ -NO enzyme via the dissociation of NAD + from a transient state, with an N-O stretching of 1,330 cm -1 and a lifetime of ca. 16 ms. Quantum mechanics/molecular mechanics calculations, based on these crystallographic and IR spectroscopic results, demonstrate that the electronic structure of I is characterized by a singly protonated Fe 3+ -NHO •- radical. The current findings provide conclusive evidence for the N 2 O generation mechanism via a radical-radical coupling of the heme nitroxyl complex with the second NO molecule.


  • Organizational Affiliation

    Graduate School of Information Sciences, Hiroshima City University, 731-3194 Hiroshima, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADP nitrous oxide-forming nitric oxide reductase
A, B
403Fusarium oxysporumMutation(s): 0 
Gene Names: CYP55A1CYP55
EC: 1.7.1.14
UniProt
Find proteins for P23295 (Fusarium oxysporum)
Explore P23295 
Go to UniProtKB:  P23295
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23295
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NO (Subject of Investigation/LOI)
Query on NO

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
NITRIC OXIDE
N O
ODUCDPQEXGNKDN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.27α = 90
b = 101.61β = 92.71
c = 73.19γ = 90
Software Package:
Software NamePurpose
CrystFELdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan19H05784
Japan Society for the Promotion of Science (JSPS)Japan19H03171

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Database references
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-29
    Changes: Refinement description