Structural Basis for the Mechanism of Respiratory Complex I

Berrisford, John M.; Sazanov, L.A.

doi:10.1074/jbc.m109.032144

Cited by 227 publications

(240 citation statements)

References 56 publications

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“…Asp-139 resides on a four-helix bundle, which is known to be conformationally flexible based on structural and inhibitorbinding studies (12,23). A likely reason for the observed behavior is the abstraction of the proton from the Asp-139/His-38 ion pair that links to the Q reduction.…”

Section: Resultsmentioning

confidence: 99%

“…1) (8,11). Biochemical and structural studies suggest that the reduction of Q activates the proton pump via a conformationaldriven coupling mechanism, accompanied by electrostatic gating (2, 6-8, [12][13][14]. A recent study suggested that water-gated transitions and cooperative electrostatic couplings are also of importance in establishing a functional pump (15).…”

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confidence: 99%

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Redox-induced activation of the proton pump in the respiratory complex I

Sharma

Belevich

Gámiz‐Hernández

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

109

170

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Complex I functions as a redox-linked proton pump in the respiratory chains of mitochondria and bacteria, driven by the reduction of quinone (Q) by NADH. Remarkably, the distance between the Q reduction site and the most distant proton channels extends nearly 200 Å. To elucidate the molecular origin of this long-range coupling, we apply a combination of large-scale molecular simulations and a site-directed mutagenesis experiment of a key residue. In hybrid quantum mechanics/molecular mechanics simulations, we observe that reduction of Q is coupled to its local protonation by the His-38/Asp-139 ion pair and Tyr-87 of subunit Nqo4. Atomistic classical molecular dynamics simulations further suggest that formation of quinol (QH 2 ) triggers rapid dissociation of the anionic Asp-139 toward the membrane domain that couples to conformational changes in a network of conserved charged residues. Site-directed mutagenesis data confirm the importance of Asp-139; upon mutation to asparagine the Q reductase activity is inhibited by 75%. The current results, together with earlier biochemical data, suggest that the proton pumping in complex I is activated by a unique combination of electrostatic and conformational transitions.NADH-quinone oxidoreductase | electron transfer | molecular dynamics simulations | QM/MM simulations | cell respiration C omplex I (NADH-quinone oxidoreductase) is the largest (550-980 kDa) and one of the most enigmatic enzymes of the electron transport chains of mitochondria and bacteria. It catalyzes electron transfer (eT) from reduced nicotinamide adenine dinucleotide (NADH) to quinone (Q) and couples the reaction to translocation of three to four protons across the membrane (1, 2). The established electrochemical proton gradient is further used to synthesize adenosine triphosphate (ATP) for active transport (3). Due to its central role in cellular respiration, elucidating the catalytic mechanism of complex I is crucial for understanding the molecular principles of biological energy transduction and for unveiling the origins of many mitochondrial disorders (4).The electrons donated by NADH to complex I are transferred via flavin mononucleotide (FMN) to Q, bound at the lower edge of the hydrophilic domain at a distance of ∼80 Å from the FMN (Fig. 1). The eT process is mediated by seven to eight iron-sulfur (FeS) clusters, depending on the organism, and takes place in ∼100 μs (5). It is believed that the eT process does not couple to proton translocation, which is likely to occur on millisecond timescales (5, 6), but it is rather the oxidoreduction chemistry of the bound Q molecule that drives the proton pump (2, 5-9; cf. ref. 10).The proton-pumping machinery of complex I is located in the membrane domain of the enzyme (9) and is responsible for pumping three to four protons across the membrane (Fig. 1) (8, 11). Biochemical and structural studies suggest that the reduction of Q activates the proton pump via a conformationaldriven coupling mechanism, accompanied by electrostatic gating (2, 6-8, 12-14). A ...

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Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Redox-induced activation of the proton pump in the respiratory complex I

Sharma

Belevich

Gámiz‐Hernández

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

109

170

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“…We have not identified any bound zinc atoms in the structure of the core hydrophilic subunits of complex I from T. thermophilus (14,16). Several NMR structures of close ␣-proteobacterial homologues of PdNUMM protein were determined by the Northeast Structural Genomics consortium.…”

Section: Discussionmentioning

confidence: 99%

Evolution of Respiratory Complex I

Yip

Harbour²,

Jayawardena³

et al. 2011

Journal of Biological Chemistry

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Modern ␣-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. Respiratory complex I from ␣-proteobacteria and mitochondria is well conserved at the level of the 14 "core" subunits, consistent with that notion. Mitochondrial complex I contains the core subunits, present in all species, and up to 31 "supernumerary" subunits, generally thought to have originated only within eukaryotic lineages. However, the full protein composition of an ␣-proteobacterial complex I has not been established previously. Here, we report the first purification and characterization of complex I from the ␣-proteobacterium Paracoccus denitrificans. Single particle electron microscopy shows that the complex has a well defined L-shape. Unexpectedly, in addition to the 14 core subunits, the enzyme also contains homologues of three supernumerary mitochondrial subunits as follows: B17.2, AQDQ/18, and 13 kDa (bovine nomenclature). This finding suggests that evolution of complex I via addition of supernumerary or "accessory" subunits started before the original endosymbiotic event that led to the creation of the eukaryotic cell. It also provides further confirmation that ␣-proteobacteria are the closest extant relatives of mitochondria.

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“…This is the NADH-binding site. In the T. thermophilus enzyme the nicotinamide ring of the bound NADH is positioned on top of the isoalloxazine ring of FMN, like in many other pyridinenucleotide-binding flavoenzymes (Berrisford and Sazanov 2009). Also the motif in the 39-kDa subunit is conserved in homologous subunits of the non-mammalian mitochondrial enzymes.…”

Section: Pyridine-nucleotide Binding Sites In Complex Imentioning

confidence: 99%

“…90Å, representing an 'electric wire' through the enzyme, nearly perpendicular to the inner membrane. The structure of the NADH-reduced enzyme nicely showed how NADH binds to FMN in the 51-kDa subunit (Berrisford and Sazanov 2009). Subunits homologous to those in the T. thermophilus enzyme are found in Complex I from many organisms.…”

Section: Introductionmentioning

confidence: 95%

The reaction of NADPH with bovine mitochondrial NADH:ubiquinone oxidoreductase revisited

Albracht

2010

J Bioenerg Biomembr

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Bovine NADH:ubiquinone oxidoreductase (Complex I) is the first complex in the mitochondrial respiratory chain. It has long been assumed that it contained only one FMN group. However, as demonstrated in 2003, the intact enzyme contains two FMN groups. The second FMN was proposed to be located in a conserved flavodoxin fold predicted to be present in the PSST subunit. The longknown reaction of Complex I with NADPH differs in many aspects from that with NADH. It was proposed that the second flavin group was specifically involved in the reaction with NADPH. The X-ray structure of the hydrophilic domain of Complex I from Thermus thermophilus (Sazanov and Hinchliffe 2006, Science 311, 1430-1436 disclosed the positions of all redox groups of that enzyme and of the subunits holding them. The PSST subunit indeed contains the predicted flavodoxin fold although it did not contain FMN. Inspired by this structure, the present paper describes a re-evaluation of the enigmatic reactions of the bovine enzyme with NADPH. Published data, as well as new freeze-quench kinetic data presented here, are incompatible with the general opinion that NADPH and NADH react at the same site. Instead, it is proposed that these pyridine nucleotides react at opposite ends of the 90Å long chain of prosthetic groups in Complex I. Ubiquinone is proposed to react with the Fe-S clusters in the TYKY subunit deep inside the hydrophilic domain. A new model for electron transfer in Complex I is proposed. In the accompanying paper this model is compared with the one advocated in current literature.

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Structural Basis for the Mechanism of Respiratory Complex I

Cited by 227 publications

References 56 publications

Redox-induced activation of the proton pump in the respiratory complex I

Redox-induced activation of the proton pump in the respiratory complex I

Evolution of Respiratory Complex I

The reaction of NADPH with bovine mitochondrial NADH:ubiquinone oxidoreductase revisited

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