9QH7 | pdb_00009qh7

NorQ in complex with NorD VWA domain steep staircase subset 1 from Paracoccus denitrificans

PDB DOI: https://doi.org/10.2210/pdb9QH7/pdb
EM Map EMD-53157: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Paracoccus denitrificans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-03-14 Released: 2026-03-25
Deposition Author(s): Kahle, M., Appelgren, S., Carroni, M., Adelroth, P., Wendler, P.
Funding Organization(s): German Research Foundation (DFG), Swedish Research Council

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

NorQD AAA+ complex drives metal insertion by a twisting mechanism.

Kahle, M., Appelgren, S., Konig, F., Carroni, M., Adelroth, P., Wendler, P.

(2026) Nat Commun 17

PubMed: 41896537 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-026-71044-4
Primary Citation Related Structures:
9QH4, 9QH6, 9QH7, 9QH8, 9QH9, 9QHD, 9QHE, 9QHF, 9QHG

PubMed Abstract:
ATPases associated with diverse cellular activities (AAA+ -ATPases) catalyse a wide range of remodelling events in all phyla. AAA+ -ATPases of the MoxR-like family typically co-operate with von Willebrand factor type A (VWA) domain containing proteins to facilitate target remodelling and metal ion insertion, but their mechanism of action is poorly understood. We studied the bacterial AAA+ -ATPase NorQ in complex with its VWA domain partner protein NorD, which are essential for nitric oxide reductase (NOR) activity. Our cryo-EM structures and biochemical analyses show that NorQ and NorD engage through two key interfaces: (i) a finger-like extension protruding from the VWA domain that penetrates the central pore of the NorQ hexamer, and (ii) the NorD C- terminus, which contacts the post-sensor 1 loop of NorQ. Our data reveal that NorQ activity remodels a linker region in NorD essential for metal insertion. Together, these findings support a model in which the NorQ complex exerts a twisting and stretching force on the NorD linker, thereby enabling metal insertion into its target NOR.

Organizational Affiliation

Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Potsdam-Golm, Germany.

Macromolecule Content

Total Structure Weight: 179.31 kDa
Atom Count: 10,180
Modeled Residue Count: 1,408
Deposited Residue Count: 1,620
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein NorQ	A, B, C, D, E A, B, C, D, E, F	270	Paracoccus denitrificans	Mutation(s): 1 Gene Names: norQ, Pden_2482
UniProt
Find proteins for Q51664 (Paracoccus denitrificans (strain Pd 1222)) Explore Q51664 Go to UniProtKB: Q51664
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q51664
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth E] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth E] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B], J [auth C], L [auth D], N [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Focus chain N [auth E]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain K [auth C] SDF format, chain I [auth B] MOL2 format, chain M [auth D] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] mmCIF format, chain M [auth D] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B]	I [auth B], K [auth C], M [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]