7DVO

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

PDB DOI: https://doi.org/10.2210/pdb7DVO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Fusarium oxysporum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-01-14 Released: 2021-05-19
Deposition Author(s): Nomura, T., Kimura, T., Kanematsu, Y., Yamashita, K., Hirata, K., Ueno, G., Murakami, H., Hisano, T., Yamagiwa, R., Takeda, H., Gopalasingam, C., Yuki, K., Kousaka, R., Yanagasawa, S., Shoji, O., Kumasaka, T., Takano, Y., Ago, H., Yamamoto, M., Sugimoto, H., Tosha, T., Kubo, M., Shiro, Y.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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

PubMed: 34001620 Search on PubMedSearch on PubMed Central
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 ₂O) 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 ₂O generation mechanism via a radical-radical coupling of the heme nitroxyl complex with the second NO molecule.

Organizational Affiliation

Graduate School of Life Science, University of Hyogo, 678-1297 Hyogo, Japan.

Macromolecule Content

Total Structure Weight: 90.69 kDa
Atom Count: 6,969
Modelled Residue Count: 798
Deposited Residue Count: 806
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADP nitrous oxide-forming nitric oxide reductase	A, B	403	Fusarium oxysporum	Mutation(s): 0 Gene Names: CYP55A1, CYP55 EC: 1.7.1.14
UniProt
Find proteins for P23295 (Fusarium oxysporum) Explore P23295 Go to UniProtKB: P23295
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23295
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B]	C [auth A], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
NO (Subject of Investigation/LOI) Query on NO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B]	D [auth A], I [auth B]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]