6M0Q

Hydroxylamine oxidoreductase from Nitrosomonas europaea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


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 of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aerobic hydroxylamine oxidoreductase
A, C, E, G, I
A, C, E, G, I, K
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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized protein
B, D, F, H, J
B, D, F, H, J, L
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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ISW
Query on ISW

Download Ideal Coordinates CCD File 
AB [auth G]
BB [auth G]
FA [auth C]
MB [auth I]
T [auth A]
AB [auth G],
BB [auth G],
FA [auth C],
MB [auth I],
T [auth A],
U [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 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
FB [auth I],
GB [auth I],
HB [auth I],
IB [auth I],
JA [auth E],
JB [auth I],
KA [auth E],
KB [auth I],
LA [auth E],
LB [auth I],
M [auth A],
MA [auth E],
N [auth A],
NA [auth E],
O [auth A],
OA [auth E],
P [auth A],
PA [auth E],
Q [auth A],
QB [auth K],
R [auth A],
RB [auth K],
S [auth A],
SB [auth K],
TA [auth G],
TB [auth K],
UA [auth G],
UB [auth K],
VA [auth G],
VB [auth K],
WA [auth G],
WB [auth K],
XA [auth G],
Y [auth C],
YA [auth G],
Z [auth C],
ZA [auth G]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
IA [auth C],
SA [auth E],
X [auth A],
ZB [auth K]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
DB [auth G]
EB [auth G]
HA [auth C]
NB [auth I]
OB [auth I]
DB [auth G],
EB [auth G],
HA [auth C],
NB [auth I],
OB [auth I],
QA [auth E],
RA [auth E],
W [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
CB [auth G]
GA [auth C]
PB [auth J]
V [auth A]
XB [auth K]
CB [auth G],
GA [auth C],
PB [auth J],
V [auth A],
XB [auth K],
YB [auth K]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.23α = 90
b = 141.91β = 90
c = 213.11γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


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: 2024-10-30
    Changes: Structure summary