6M0P | pdb_00006m0p

Hydroxylamine oxidoreductase in complex with juglone

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 
    0.292 (Depositor), 0.295 (DCC) 
  • R-Value Work: 
    0.256 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 
    0.258 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Juglone, a plant-derived 1,4-naphthoquinone, binds to hydroxylamine oxidoreductase and inhibits the electron transfer to cytochrome c 554.

Akutsu, Y., Fujiwara, T., Suzuki, R., Nishigaya, Y., Yamazaki, T.

(2023) Appl Environ Microbiol 89: e0129123-e0129123

  • DOI: https://doi.org/10.1128/aem.01291-23
  • Primary Citation Related Structures: 
    6M0P, 6M0Q

  • PubMed Abstract: 

    Nitrification, the microbial conversion of ammonia to nitrate via nitrite, plays a pivotal role in the global nitrogen cycle. However, the excessive use of ammonium-based fertilizers in agriculture has disrupted this cycle, leading to groundwater pollution and greenhouse gas emissions. In this study, we have demonstrated the inhibitory effects of plant-derived juglone and related 1,4-naphthoquinones on the nitrification process in Nitrosomonas europaea . Notably, the inhibition mechanism is elucidated in which 1,4-naphthoquinones interact with hydroxylamine oxidoreductase, disrupting the electron transfer to cytochrome c 554 , a physiological electron acceptor. These findings support the notion that phytochemicals can impede nitrification by interfering with the essential electron transfer process in ammonia oxidation. The findings presented in this article offer valuable insights for the development of strategies aimed at the management of nitrification, reduction of fertilizer utilization, and mitigation of greenhouse gas emissions.

    • Organizational Affiliation: 
    • Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan.

Macromolecule Content 

  • Total Structure Weight: 238.11 kDa 
  • Atom Count: 14,521 
  • Modeled Residue Count: 1,677 
  • Deposited Residue Count: 1,983 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Aerobic hydroxylamine oxidoreductase
A, C, E
570Nitrosomonas europaeaMutation(s): 0 
EC: 1.7.2.6 (UniProt), 1.7.2.9 (UniProt)
UniProt
Find proteins for Q50925 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298))
Explore Q50925 
Go to UniProtKB:  Q50925
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ50925
Sequence Annotations
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Reference Sequence
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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Uncharacterized protein
B, D, F
91Nitrosomonas europaeaMutation(s): 0 
UniProt
Find proteins for Q82V11 (Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298))
Explore Q82V11 
Go to UniProtKB:  Q82V11
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ82V11
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ISW

Query on ISW


Download:Ideal Coordinates CCD File
BA [auth C],
N [auth A],
Q [auth A]		{3,3'-[(9S)-8,13-diethenyl-3,7,12,17-tetramethyl-9,10-dihydroporphyrin-2,18-diyl-kappa~4~N~21~,N~22~,N~23~,N~24~]dipropanoato(2-)}iron
C34 H34 Fe N4 O4
QSWMAEGFLATCMU-JMAPEOGHSA-L
HEC

Query on HEC


Download:Ideal Coordinates CCD File
CA [auth E]
DA [auth E]
EA [auth E]
FA [auth E]
G [auth A]
CA [auth E],
DA [auth E],
EA [auth E],
FA [auth E],
G [auth A],
GA [auth E],
H [auth A],
HA [auth E],
I [auth A],
IA [auth E],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
1PE

Query on 1PE


Download:Ideal Coordinates CCD File
AA [auth C],
Z [auth C]		PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
JUG
(Subject of Investigation/LOI)

Query on JUG


Download:Ideal Coordinates CCD File
JA [auth E],
Y [auth C]		5-hydroxynaphthalene-1,4-dione
C10 H6 O3
KQPYUDDGWXQXHS-UHFFFAOYSA-N
PEG

Query on PEG


Download:Ideal Coordinates CCD File
KA [auth E],
O [auth A],
P [auth A]		DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free:  0.292 (Depositor), 0.295 (DCC) 
  • R-Value Work:  0.256 (Depositor), 0.258 (DCC) 
  • R-Value Observed: 0.258 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.34α = 90
b = 141.07β = 90
c = 106.09γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-10
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-05-08
    Changes: Database references
  • Version 1.3: 2025-09-17
    Changes: Advisory, Derived calculations, Structure summary