28PQ | pdb_000028pq

CryoEM structure of native quinol dependent Nitric Oxide Reductase Trp718Ala variant at pH 6.5 on gold grid.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 28PQ

This is version 1.0 of the entry. See complete history

Literature

CryoEM Structures of Native Quinol-Dependent Nitric Oxide Reductase in Resting and Quinol-Bound States.

Khaja, F.T.Mboukou, A.Aspinall, L.P.Hawksworth, C.E.Eady, R.R.Antonyuk, S.V.Muench, S.P.Hasnain, S.S.

(2026) ACS Bio Med Chem Au 6: 145-159

  • DOI: https://doi.org/10.1021/acsbiomedchemau.5c00245
  • Primary Citation Related Structures: 
    28PN, 28PP, 28PQ, 28PR, 9ST9, 9STA

  • PubMed Abstract: 

    The membrane-bound quinol-dependent nitric oxide reductases (qNORs), which are members of the respiratory heme-copper oxidase superfamily, are of major importance to food production, environment, and human health. They are unique to bacteria and catalyze N-N bond formation, converting nitric oxide (NO) to generate the enzymatic product, nitrous oxide (N 2 O), in agricultural and pathogenic conditions. High-resolution qNOR structures have been reported from two bacterial species, in which the molecular size of the protein was increased by the insertion of apocytochrome b 562 (BRIL) at the C-terminus to facilitate cryoEM structure determination. However, it remains uncertain how BRIL fusion alters the native structure of these metalloenzymes. Here, we present the first high-resolution structure of Achromobacter xylosoxidans qNOR ( Ax qNOR) determined without a fusion tag at two different pH values, revealing structural differences near the catalytic core as well as overall conformational changes between the native and fusion-tagged structures. The native enzyme shows a bell-shaped pH dependence of enzymatic activity, like nitrite reductase, the preceding enzyme in the denitrification pathway, which generates the substrate NO. In addition, we report structures of Ax qNOR bound to quinol and hydroxyquinol that provide valuable insight into the potential electron transfer pathway originating from Trp718 to the redox centers.


  • Organizational Affiliation
    • Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.

Macromolecule Content 

  • Total Structure Weight: 173.93 kDa 
  • Atom Count: 12,350 
  • Modeled Residue Count: 1,421 
  • Deposited Residue Count: 1,522 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nitric oxide reductase subunit B
A, B
761Achromobacter xylosoxidansMutation(s): 1 
Gene Names: norB_1ERS451415_02175IUJ48_17015
EC: 1.7.2.5
UniProt
Find proteins for A0ABF7PH53 (Alcaligenes xylosoxydans xylosoxydans)
Explore A0ABF7PH53 
Go to UniProtKB:  A0ABF7PH53
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ABF7PH53
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
(Subject of Investigation/LOI)

Query on HEM



Download:Ideal Coordinates CCD File
C [auth A],
E [auth A],
I [auth B],
K [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
UQ5
(Subject of Investigation/LOI)

Query on UQ5



Download:Ideal Coordinates CCD File
H [auth B]2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE
C34 H50 O4
NYFAQDMDAFCWPU-UVCHAVPFSA-N
LMT
(Subject of Investigation/LOI)

Query on LMT



Download:Ideal Coordinates CCD File
G [auth A],
M [auth B],
N [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/X015491/1

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-06
    Type: Initial release