8BGW

CryoEM structure of quinol-dependent Nitric Oxide Reductase (qNOR) from Alcaligenes xylosoxidans at 2.2 A resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A 2.2 angstrom cryoEM structure of a quinol-dependent NO Reductase shows close similarity to respiratory oxidases.

Flynn, A.J.Antonyuk, S.V.Eady, R.R.Muench, S.P.Hasnain, S.S.

(2023) Nat Commun 14: 3416-3416

  • DOI: https://doi.org/10.1038/s41467-023-39140-x
  • Primary Citation of Related Structures:  
    8BGW

  • PubMed Abstract: 

    Quinol-dependent nitric oxide reductases (qNORs) are considered members of the respiratory heme-copper oxidase superfamily, are unique to bacteria, and are commonly found in pathogenic bacteria where they play a role in combating the host immune response. qNORs are also essential enzymes in the denitrification pathway, catalysing the reduction of nitric oxide to nitrous oxide. Here, we determine a 2.2 Å cryoEM structure of qNOR from Alcaligenes xylosoxidans, an opportunistic pathogen and a denitrifying bacterium of importance in the nitrogen cycle. This high-resolution structure provides insight into electron, substrate, and proton pathways, and provides evidence that the quinol binding site not only contains the conserved His and Asp residues but also possesses a critical Arg (Arg720) observed in cytochrome bo 3 , a respiratory quinol oxidase.


  • Organizational Affiliation

    School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nitric oxide reductase subunit B
A, B
761Achromobacter xylosoxidansMutation(s): 0 
Gene Names: norB_1ERS451415_02175I6G72_25885
EC: 1.7.2.5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LOP
Query on LOP

Download Ideal Coordinates CCD File 
AA [auth B]
I [auth A]
J [auth A]
K [auth A]
L [auth A]
AA [auth B],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [auth B]
(1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE
C35 H68 N O8 P
FUUNMZKPCMPCHT-ILGKRYBBSA-N
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
Q [auth B],
R [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
10M
Query on 10M

Download Ideal Coordinates CCD File 
G [auth A],
P [auth B]
decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside
C22 H42 O10 S
YZNNXXWNKQOETJ-HYLFJBCQSA-N
UQ1
Query on UQ1

Download Ideal Coordinates CCD File 
H [auth A],
U [auth B]
UBIQUINONE-1
C14 H18 O4
SOECUQMRSRVZQQ-UHFFFAOYSA-N
FE (Subject of Investigation/LOI)
Query on FE

Download Ideal Coordinates CCD File 
E [auth A],
S [auth B]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A],
T [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC5.8.0267
MODEL REFINEMENTPHENIX1.2
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom108466/Z/15/Z
Wellcome TrustUnited Kingdom221524/Z/20/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release