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Structure paper

TitleKey role of quinone in the mechanism of respiratory complex I.
Journal, issue, pagesNat Commun, Vol. 11, Issue 1, Page 4135, Year 2020
Publish dateAug 18, 2020
AuthorsJavier Gutiérrez-Fernández / Karol Kaszuba / Gurdeep S Minhas / Rozbeh Baradaran / Margherita Tambalo / David T Gallagher / Leonid A Sazanov /
PubMed AbstractComplex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in ...Complex I is the first and the largest enzyme of respiratory chains in bacteria and mitochondria. The mechanism which couples spatially separated transfer of electrons to proton translocation in complex I is not known. Here we report five crystal structures of T. thermophilus enzyme in complex with NADH or quinone-like compounds. We also determined cryo-EM structures of major and minor native states of the complex, differing in the position of the peripheral arm. Crystal structures show that binding of quinone-like compounds (but not of NADH) leads to a related global conformational change, accompanied by local re-arrangements propagating from the quinone site to the nearest proton channel. Normal mode and molecular dynamics analyses indicate that these are likely to represent the first steps in the proton translocation mechanism. Our results suggest that quinone binding and chemistry play a key role in the coupling mechanism of complex I.
External linksNat Commun / PubMed:32811817 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution3.109 - 6.1 Å
Structure data

11231

6ziy

EMDB-11231, PDB-6ziy:
Respiratory complex I from Thermus thermophilus, NADH dataset, major state
Method: EM (single particle) / Resolution: 4.25 Å

11235

6zjl

EMDB-11235, PDB-6zjl:
Respiratory complex I from Thermus thermophilus, NAD+ dataset, major state
Method: EM (single particle) / Resolution: 4.3 Å

11237

6zjn

EMDB-11237, PDB-6zjn:
Respiratory complex I from Thermus thermophilus, NADH dataset, minor state
Method: EM (single particle) / Resolution: 6.1 Å

11238

6zjy

EMDB-11238, PDB-6zjy:
Respiratory complex I from Thermus thermophilus, NAD+ dataset, minor state
Method: EM (single particle) / Resolution: 5.5 Å

PDB-6i0d:
Respiratory complex I from Thermus thermophilus with bound Decyl-Ubiquinone
Method: X-RAY DIFFRACTION / Resolution: 3.6 Å

PDB-6i1p:
Respiratory complex I from Thermus thermophilus with bound NADH
Method: X-RAY DIFFRACTION / Resolution: 3.207 Å

PDB-6q8o:
Respiratory complex I from Thermus thermophilus with bound Piericidin A
Method: X-RAY DIFFRACTION / Resolution: 3.605 Å

PDB-6q8w:
Respiratory complex I from Thermus thermophilus with bound Aureothin.
Method: X-RAY DIFFRACTION / Resolution: 3.4 Å

PDB-6q8x:
Respiratory complex I from Thermus thermophilus with bound Pyridaben.
Method: X-RAY DIFFRACTION / Resolution: 3.508 Å

PDB-6y11:
Respiratory complex I from Thermus thermophilus
Method: X-RAY DIFFRACTION / Resolution: 3.109 Å

Chemicals

ChemComp-SF4:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

ChemComp-FMN:
FLAVIN MONONUCLEOTIDE / Flavin mononucleotide

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster

ChemComp-DCQ:
2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione

ChemComp-NAI:
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Nicotinamide adenine dinucleotide

ChemComp-HQH:
Piericidin A / antibiotic*YM / Piericidin A

ChemComp-HQW:
Aureothin / antitumor, antifungal, antibiotic*YM / Aureothin

ChemComp-HQK:
Pyridaben

Source
  • thermus thermophilus (bacteria)
  • thermus thermophilus hb8 (bacteria)
  • thermus thermophilus (strain hb8 / atcc 27634 / dsm 579) (bacteria)
KeywordsMEMBRANE PROTEIN / Respiratory chain / complex I / NADH:ubiquinone oxidoreductase / electron transfer / proton translocation

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