7F76 | pdb_00007f76

Crystal Structure of FMN-dependent NADPH-quinone reductase (azoR) from Bacillus cohnii

PDB DOI: https://doi.org/10.2210/pdb7F76/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sutcliffiella cohnii
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-06-28 Released: 2022-05-11
Deposition Author(s): Yoneda, K., Sakuraba, H., Ohshima, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.57 Å
R-Value Free:
0.191 (Depositor), 0.210 (DCC)
R-Value Work:
0.165 (Depositor), 0.180 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural and Functional Characteristics of FMN-Dependent NADPH-Indigo Reductase Homolog from Bacillus cohnii.

Yoneda, K., Sakuraba, H., Hayashi, J., Naruse, Y., Araki, T., Ohshima, T.

(2025) J Nutr Sci Vitaminol (Tokyo) 71: 180-183

PubMed: 40301060 Search on PubMed
DOI: https://doi.org/10.3177/jnsv.71.180
Primary Citation of Related Structures:
7F76

PubMed Abstract:
We found indigo reductase homolog in Bacillus cohnii gene and succeeded in production of a large amount of the recombinant homolog in Escherichia coli. The homolog exhibited FMN-dependent NADPH-quinone reductase activity, but not indigo-reducing activity. Crystal structure analysis of the enzyme revealed the formation of a binary complex with FMN, 2-propanol, and glycerol, determined at a resolution of 1.57 Å. Notably, the structure of FMN was of particular interest, as the isoalloxazine ring of FMN exhibited a butterfly-like bent conformation, with an angular deviation of approximately 9.4º to 10.9º along the axis between N5 and N10. The reason for FMN adopting a butterfly-like structure was thought that the exposure of the enzyme crystal to X-ray radiation led to the one-electron reduction of FMN, forming the semiquinone radical FMNH ^•.

Organizational Affiliation

Department of Food and Life Sciences, School of Agriculture, Tokai University.

Macromolecule Content

Total Structure Weight: 45.01 kDa
Atom Count: 3,060
Modeled Residue Count: 345
Deposited Residue Count: 392
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FMN-dependent NADPH-quinone reductase (azoR)	A, B	196	Sutcliffiella cohnii	Mutation(s): 0 Gene Names: azoR
UniProt
Find proteins for A0A223KLJ1 (Sutcliffiella cohnii) Explore A0A223KLJ1 Go to UniProtKB: A0A223KLJ1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A223KLJ1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
IPA Query on IPA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A], F [auth A], H [auth B], J [auth B], K [auth B]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B] Focus chain K [auth B]