Limits...
Crystal structure of the entire respiratory complex I.

Baradaran R, Berrisford JM, Minhas GS, Sazanov LA - Nature (2013)

Bottom Line: Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues.The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements.The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.

View Article: PubMed Central - PubMed

Affiliation: Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.

ABSTRACT
Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.

Show MeSH

Related in: MedlinePlus

a) E-channel (fourth proton translocation channel). Charged and polar residues constituting the channel are shown as sticks. Central residues are shown with carbon in yellow, those forming a link to the Q site in magenta, link to the cytoplasm in blue, link to the periplasm in green and those interacting with quinone headgroup in cyan. Key residues are labelled, with Glu/Asp quartet in red. Approximate proton translocation path is indicated by blue arrow. Quinone cavity is shown with surface in brown. b) Central axis of charged and polar residues. Residues shown are either central to half-channels or are forming the connection between them (charged residues have carbon in magenta, polar in cyan). Most of them are located near the breaks in key helices TM7/8/12 (antiporters), 10_TM3 and 8_TM5. Predicted waters nearby, modelled using Dowser software44, are shown as spheres. Connecting elements are shown in solid colours: helix HL in magenta and the βH element in blue, with the C-terminal helix CH29 and the β-hairpin from each antiporter labelled. The contacting Nqo10 helix is labelled 10_H. Subunits are coloured as in Fig. 1.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3672946&req=5

Figure 3: a) E-channel (fourth proton translocation channel). Charged and polar residues constituting the channel are shown as sticks. Central residues are shown with carbon in yellow, those forming a link to the Q site in magenta, link to the cytoplasm in blue, link to the periplasm in green and those interacting with quinone headgroup in cyan. Key residues are labelled, with Glu/Asp quartet in red. Approximate proton translocation path is indicated by blue arrow. Quinone cavity is shown with surface in brown. b) Central axis of charged and polar residues. Residues shown are either central to half-channels or are forming the connection between them (charged residues have carbon in magenta, polar in cyan). Most of them are located near the breaks in key helices TM7/8/12 (antiporters), 10_TM3 and 8_TM5. Predicted waters nearby, modelled using Dowser software44, are shown as spheres. Connecting elements are shown in solid colours: helix HL in magenta and the βH element in blue, with the C-terminal helix CH29 and the β-hairpin from each antiporter labelled. The contacting Nqo10 helix is labelled 10_H. Subunits are coloured as in Fig. 1.

Mentions: In Nqo8, charged residues are found in similar positions to key antiporters’ residues: Glu130/Glu163 in the GluTM5 position, Glu213/Glu248 - near LysTM7 (Fig. 2c). Overall, Nqo8 contains many more charged residues in the membrane (Fig. 3a) than the antiporters, and many of these residues (including Glu163 and Glu213) are conserved in complex I and in membrane-bound hydrogenases (Supplementary Figs. 1 and 6). They form an unusual chain (or “funnel”) of charged residues leading from the Q-binding site to a remarkable network of four interacting carboxylates deep in the membrane (Glu130, Glu163 and Glu213 from Nqo8 plus conserved 7_Asp72 (prefix indicates subunit)). The charged network congregates around the highly conserved broken 10_TM3, a hotspot for human disease mutations29. On the other side of the break, conserved 10_Tyr59 interacts with essential 11_Glu32, part of a fourth proton translocation channel proposed previously29. Nqo11 superimposes with helices 4-6 from the antiporter half-channels, overlaying Glu32 with GluTM529.


Crystal structure of the entire respiratory complex I.

Baradaran R, Berrisford JM, Minhas GS, Sazanov LA - Nature (2013)

a) E-channel (fourth proton translocation channel). Charged and polar residues constituting the channel are shown as sticks. Central residues are shown with carbon in yellow, those forming a link to the Q site in magenta, link to the cytoplasm in blue, link to the periplasm in green and those interacting with quinone headgroup in cyan. Key residues are labelled, with Glu/Asp quartet in red. Approximate proton translocation path is indicated by blue arrow. Quinone cavity is shown with surface in brown. b) Central axis of charged and polar residues. Residues shown are either central to half-channels or are forming the connection between them (charged residues have carbon in magenta, polar in cyan). Most of them are located near the breaks in key helices TM7/8/12 (antiporters), 10_TM3 and 8_TM5. Predicted waters nearby, modelled using Dowser software44, are shown as spheres. Connecting elements are shown in solid colours: helix HL in magenta and the βH element in blue, with the C-terminal helix CH29 and the β-hairpin from each antiporter labelled. The contacting Nqo10 helix is labelled 10_H. Subunits are coloured as in Fig. 1.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3672946&req=5

Figure 3: a) E-channel (fourth proton translocation channel). Charged and polar residues constituting the channel are shown as sticks. Central residues are shown with carbon in yellow, those forming a link to the Q site in magenta, link to the cytoplasm in blue, link to the periplasm in green and those interacting with quinone headgroup in cyan. Key residues are labelled, with Glu/Asp quartet in red. Approximate proton translocation path is indicated by blue arrow. Quinone cavity is shown with surface in brown. b) Central axis of charged and polar residues. Residues shown are either central to half-channels or are forming the connection between them (charged residues have carbon in magenta, polar in cyan). Most of them are located near the breaks in key helices TM7/8/12 (antiporters), 10_TM3 and 8_TM5. Predicted waters nearby, modelled using Dowser software44, are shown as spheres. Connecting elements are shown in solid colours: helix HL in magenta and the βH element in blue, with the C-terminal helix CH29 and the β-hairpin from each antiporter labelled. The contacting Nqo10 helix is labelled 10_H. Subunits are coloured as in Fig. 1.
Mentions: In Nqo8, charged residues are found in similar positions to key antiporters’ residues: Glu130/Glu163 in the GluTM5 position, Glu213/Glu248 - near LysTM7 (Fig. 2c). Overall, Nqo8 contains many more charged residues in the membrane (Fig. 3a) than the antiporters, and many of these residues (including Glu163 and Glu213) are conserved in complex I and in membrane-bound hydrogenases (Supplementary Figs. 1 and 6). They form an unusual chain (or “funnel”) of charged residues leading from the Q-binding site to a remarkable network of four interacting carboxylates deep in the membrane (Glu130, Glu163 and Glu213 from Nqo8 plus conserved 7_Asp72 (prefix indicates subunit)). The charged network congregates around the highly conserved broken 10_TM3, a hotspot for human disease mutations29. On the other side of the break, conserved 10_Tyr59 interacts with essential 11_Glu32, part of a fourth proton translocation channel proposed previously29. Nqo11 superimposes with helices 4-6 from the antiporter half-channels, overlaying Glu32 with GluTM529.

Bottom Line: Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues.The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements.The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.

View Article: PubMed Central - PubMed

Affiliation: Medical Research Council Mitochondrial Biology Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.

ABSTRACT
Complex I is the first and largest enzyme of the respiratory chain and has a central role in cellular energy production through the coupling of NADH:ubiquinone electron transfer to proton translocation. It is also implicated in many common human neurodegenerative diseases. Here, we report the first crystal structure of the entire, intact complex I (from Thermus thermophilus) at 3.3 Å resolution. The structure of the 536-kDa complex comprises 16 different subunits, with a total of 64 transmembrane helices and 9 iron-sulphur clusters. The core fold of subunit Nqo8 (ND1 in humans) is, unexpectedly, similar to a half-channel of the antiporter-like subunits. Small subunits nearby form a linked second half-channel, which completes the fourth proton-translocation pathway (present in addition to the channels in three antiporter-like subunits). The quinone-binding site is unusually long, narrow and enclosed. The quinone headgroup binds at the deep end of this chamber, near iron-sulphur cluster N2. Notably, the chamber is linked to the fourth channel by a 'funnel' of charged residues. The link continues over the entire membrane domain as a flexible central axis of charged and polar residues, and probably has a leading role in the propagation of conformational changes, aided by coupling elements. The structure suggests that a unique, out-of-the-membrane quinone-reaction chamber enables the redox energy to drive concerted long-range conformational changes in the four antiporter-like domains, resulting in translocation of four protons per cycle.

Show MeSH
Related in: MedlinePlus