8BGW | pdb_00008bgw

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

PDB DOI: https://doi.org/10.2210/pdb8BGW/pdb
EM Map EMD-16041: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Achromobacter xylosoxidans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-10-28 Released: 2023-08-16
Deposition Author(s): Flynn, A., Antonyuk, S.V., Eady, R.R., Muench, S.P., Hasnain, S.S.
Funding Organization(s): Wellcome Trust

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

PubMed: 37296134 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-39140-x
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 182.21 kDa
Atom Count: 12,927
Modeled Residue Count: 1,500
Deposited Residue Count: 1,522
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitric oxide reductase subunit B	A, B	761	Achromobacter xylosoxidans	Mutation(s): 0 Gene Names: norB_1, ERS451415_02175, I6G72_25885 EC: 1.7.2.5

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LOP Query on LOP Download:Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain AA [auth B]	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		Interactions Focus chain AA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], Q [auth B], R [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain Q [auth B] Focus chain R [auth B]
10M Query on 10M Download:Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A]	G [auth A], P [auth B]	decyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside C₂₂ H₄₂ O₁₀ S YZNNXXWNKQOETJ-HYLFJBCQSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]
UQ1 Query on UQ1 Download:Ideal Coordinates CCD File SDF format, chain U [auth B] SDF format, chain H [auth A] MOL2 format, chain U [auth B] MOL2 format, chain H [auth A] mmCIF format, chain U [auth B] mmCIF format, chain H [auth A]	H [auth A], U [auth B]	UBIQUINONE-1 C₁₄ H₁₈ O₄ SOECUQMRSRVZQQ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain U [auth B]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain S [auth B] SDF format, chain E [auth A] MOL2 format, chain S [auth B] MOL2 format, chain E [auth A] mmCIF format, chain S [auth B] mmCIF format, chain E [auth A]	E [auth A], S [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain S [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain F [auth A] MOL2 format, chain T [auth B] MOL2 format, chain F [auth A] mmCIF format, chain T [auth B] mmCIF format, chain F [auth A]	F [auth A], T [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain T [auth B] Interactions & Density Focus chain F [auth A] Focus chain T [auth B]