6Q9G

Crystal structure of reduced Aquifex aeolicus NADH-quinone oxidoreductase subunits NuoE G129D and NuoF bound to NADH

PDB DOI: https://doi.org/10.2210/pdb6Q9G/pdb

Classification: OXIDOREDUCTASE
Organism(s): Aquifex aeolicus VF5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2018-12-18 Released: 2019-06-26
Deposition Author(s): Wohlwend, D., Gerhardt, S., Gnandt, E., Friedrich, T.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.231
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A mechanism to prevent production of reactive oxygen species by Escherichia coli respiratory complex I.

Schulte, M., Frick, K., Gnandt, E., Jurkovic, S., Burschel, S., Labatzke, R., Aierstock, K., Fiegen, D., Wohlwend, D., Gerhardt, S., Einsle, O., Friedrich, T.

(2019) Nat Commun 10: 2551-2551

PubMed: 31186428 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-019-10429-0
Primary Citation of Related Structures:
6HL2, 6HL3, 6HL4, 6HLA, 6HLI, 6HLJ, 6HLM, 6Q9C, 6Q9G, 6Q9J, 6Q9K, 6R7P

PubMed Abstract:
Respiratory complex I plays a central role in cellular energy metabolism coupling NADH oxidation to proton translocation. In humans its dysfunction is associated with degenerative diseases. Here we report the structure of the electron input part of Aquifex aeolicus complex I at up to 1.8 Å resolution with bound substrates in the reduced and oxidized states. The redox states differ by the flip of a peptide bond close to the NADH binding site. The orientation of this peptide bond is determined by the reduction state of the nearby [Fe-S] cluster N1a. Fixation of the peptide bond by site-directed mutagenesis led to an inactivation of electron transfer and a decreased reactive oxygen species (ROS) production. We suggest the redox-gated peptide flip to represent a previously unrecognized molecular switch synchronizing NADH oxidation in response to the redox state of the complex as part of an intramolecular feed-back mechanism to prevent ROS production.

Organizational Affiliation

Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany.

Macromolecule Content

Total Structure Weight: 138.34 kDa
Atom Count: 10,337
Modelled Residue Count: 1,146
Deposited Residue Count: 1,188
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit E	A, C	160	Aquifex aeolicus VF5	Mutation(s): 1 Gene Names: nuoE, aq_574 EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
UniProt
Find proteins for O66842 (Aquifex aeolicus (strain VF5)) Explore O66842 Go to UniProtKB: O66842
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O66842
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NADH-quinone oxidoreductase subunit F	B, D	434	Aquifex aeolicus VF5	Mutation(s): 0 Gene Names: nuoF, aq_573 EC: 1.6.5.11 (PDB Primary Data), 7.1.1 (UniProt)
UniProt
Find proteins for O66841 (Aquifex aeolicus (strain VF5)) Explore O66841 Go to UniProtKB: O66841
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O66841
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain S [auth D] MOL2 format, chain J [auth B] MOL2 format, chain S [auth D] mmCIF format, chain J [auth B] mmCIF format, chain S [auth D]	J [auth B], S [auth D]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain J [auth B] Focus chain S [auth D] Interactions & Density Focus chain J [auth B] Focus chain S [auth D]
FMN Query on FMN Download Ideal Coordinates CCD File SDF format, chain R [auth D] SDF format, chain I [auth B] MOL2 format, chain R [auth D] MOL2 format, chain I [auth B] mmCIF format, chain R [auth D] mmCIF format, chain I [auth B]	I [auth B], R [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain I [auth B] Focus chain R [auth D] Interactions & Density Focus chain I [auth B] Focus chain R [auth D]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain Q [auth D] MOL2 format, chain H [auth B] MOL2 format, chain Q [auth D] mmCIF format, chain H [auth B] mmCIF format, chain Q [auth D]	H [auth B], Q [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain Q [auth D] Interactions & Density Focus chain H [auth B] Focus chain Q [auth D]
FES Query on FES Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth C] MOL2 format, chain E [auth A] MOL2 format, chain N [auth C] mmCIF format, chain E [auth A] mmCIF format, chain N [auth C]	E [auth A], N [auth C]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain N [auth C] Interactions & Density Focus chain E [auth A] Focus chain N [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain U [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D]	F [auth A], G [auth A], O [auth C], P [auth C], U [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain T [auth D] MOL2 format, chain K [auth B] MOL2 format, chain T [auth D] mmCIF format, chain K [auth B] mmCIF format, chain T [auth D]	K [auth B], T [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain T [auth D] Interactions & Density Focus chain K [auth B] Focus chain T [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain V [auth D] SDF format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain V [auth D] MOL2 format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain V [auth D] mmCIF format, chain L [auth B]	L [auth B], M [auth B], V [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain M [auth B] Focus chain V [auth D] Interactions & Density Focus chain L [auth B] Focus chain M [auth B] Focus chain V [auth D]