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• Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter
• Jimmy Van M
• Mise à jour => Proton-5.5-GE-1
• proton-call: error: proton.conf does not exist - proton-caller
• Deadly Colorado blaze renews focus on underground coal fires
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• Charged Particles
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• Proton Mining Calculator & Profitability Calculator

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Structure and mechanism of the Mrp complex, an ancient cation/proton antiporter

Try out PMC Labs and tell us what you think. Learn More. Steiner J, Sazanov LA. Structure of the Mrp antiporter complex. Electron Microscopy Data Bank. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each.

Surface charge distribution within each monomer is remarkably asymmetric, revealing probable proton and sodium translocation pathways. On the basis of the structure we propose a mechanism where the coupling between sodium and proton translocation is facilitated by a series of electrostatic interactions between a cation and key charged residues. This mechanism is likely to be applicable to the entire family of redox proton pumps, where electron transfer to substrates replaces cation movements.

Several protein families catalyse this reaction and are mostly encoded by a single gene, such as the NHE family in eukaryotes and the NhaA family in bacteria Krulwich et al. For example, the stoichiometry for E. The exact value for Mrp has not been fully established experimentally due to challenges in purification of the intact complex Morino et al. This raises the question as to why a so much more complicated protein assembly is needed to catalyse a similar reaction. Since under the extreme environmental conditions Mrp is essential for cell survival and cannot be replaced by single subunit antiporters Cheng et al.

Their homologues called antiporter-like subunits, which we will abbreviate to APLS are found in many proton-pumping protein complexes where they are present in one to three and recently discovered four [ Chadwick et al. These include bacterial Baradaran et al. These modern enzymes represent some of the largest membrane protein complexes known and are thought to have evolved from the unification of the membrane transporter Mrp-like module with the soluble NiFe-hydrogenase module, sometimes followed by the addition of an electron input module, such as the NAD-linked formate dehydrogenase in case of complex I Efremov and Sazanov, The Mrp complex thus represents an ancient ancestor of diverse protein families and is thought to have been among the few membrane proteins present in the last common ancestor of prokaryotes Sousa et al.

Structures of complex I Agip et al. These enzymes consist of two main domains — the Mrp-like membrane domain, responsible for proton translocation or sodium in case of MBH and an attached hydrophilic redox domain, responsible for electron transfer between substrates e. NADH to quinone in case of complex I. Upon solving the first structures of complex I, we proposed that redox reactions may drive proton translocation via long-range conformational changes Baradaran et al.

However, such changes have not been visualized till now despite significant efforts Parey et al. Electrostatic interactions between the key charged residues have also been proposed to play an additional Efremov and Sazanov, or main Kaila, ; Verkhovskaya and Bloch, role in the mechanism.

The structure of the universal common ancestor of these enzymes, the Mrp complex, has been lacking so far. Clearly, it would be instrumental in resolving the coupling mechanism, which should have common principles for this huge group of protein families. Furthermore, inactivation of the Mrp complex strongly reduces pathogenicity of such problematic human pathogens as S. To address these questions, we have determined the first, to our knowledge, atomic structure of the Mrp complex.

The Mrp complex from Anoxybacillus flavithermus shows high sequence similarity to the well-characterised Mrp complexes from Bacillus sp Figure 4—figure supplements 3 — 4.

The His-tagged Mrp complex from A. It showed higher apparent stability than the Bacillus complex Morino et al. The protein tended to aggregate heavily in ice holes of cryo-EM grids. Therefore, we used grids coated with a very thin layer of continuous carbon, which resulted in a uniform particle distribution Figure 1—figure supplement 2. However, the particles showed a strong preferred orientation, with the hydrophilic protein surface attached to the carbon.

To compensate for the associated loss of information, data collection was performed with grids tilted Tan et al. Particles appeared as dimers of only approximate C2 symmetry as the angle between monomers varied, resulting in several 3D classes differing by that angle. After symmetry expansion in C2 point group in Relion, resulting pseudo-monomer particles could be refined to 3. This allowed initial model building for most of the model, however, cryo-EM density at the edges of the monomer was fuzzy, with some TM helices TMH in the distal part of MrpA completely disordered.

Comparisons of cryo-EM maps of various dimers did not reveal any specific differences in the overall structure, apart from different apparent angles between the monomers.

The best dimer class refined to 3. Side view and view from the cytoplasm, where two N-terminal helices of subunit MrpE, forming most of the dimer interface, are circled. Homologs of Mrp subunits are coloured similarly as in c , with an additional MrpD-like subunit in complex I in orange.

Two modules based on the Mrp structure are indicated. The size exclusion elution profile is shown, with LMNG as detergent. The fraction in the middle of the dimer peak which eluted at around The elution peaks of the dimer and monomer are highlighted in blue and green, respectively.

The elution of the dimer is highlighted in blue. Non-transformed KNabc vesicles were used as a control at pH 8. The results are averages from three independent preparations. The error bars show the standard deviations of the means. Non-transformed KNabc cells were used as a control.

The results are averages from three independent experiments. Representative raw micrograph is shown with some of picked particles circled. After classification, the two best classes were either further classified to process the Mrp dimer, or symmetry expanded according to the C2 point group to process the Mrp monomer. Further 3D classifications and 3D auto-refinements resulted in three different dimer classes with distinct angles between the monomers of the dimer and indicated resolutions.

After classification, the best class was either further classified to process the Mrp dimer, or 3D auto-refined and symmetry expanded according to the C2 point group to process the Mrp monomer.

The symmetry expanded particles were further classified to process the Mrp monomer, resulting in two good classes. The fold of these Mrp subunits is extremely well preserved in MBH, including all the key residues, which are conserved and essential for activity Figure 3a,c , Supplementary file 1.

MrpE caps the structure and is involved in dimerization. Apparent extent of the lipid membrane is outlined. Top is side view with cytosolic side up. Likely areas of interactions with protons and sodium and are indicated. Amphipathic helix HL from subunit MrpA is indicated. Amphipathic helix AH from subunit MrpE is indicated. The surface of one monomer is shown with surface-exposed residues coloured according to Eisenberg hydrophobicity scale from white hydrophobic to red hydrophilic.

The second monomer is shown in cartoon only. Protein density is in magenta, while the detergent belt is in grey. Alignments to MBH are in the left column and to complex I in the right column. The top row shows view from the cytosol, with the conserved domains underlined. In the bottom row only MBH and complex I are shown in the same orientation as above, with subunits homologous to Mrp coloured as in Mrp and the rest grey.

MBH has its redox module attached to the Mrp-like domain on the opposite side compared to complex I. Except for MrpD, suffixes indicate subunit. The similarity to complex I extends to the entire MrpA, MrpD and MrpC subunits, with the fold and many key residues well conserved Figure 3a,b , Supplementary file 1 and Figure 4—figure supplement 2b.

These residues are likely the key to proton translocation because they are absolutely conserved, essential for activity and sit in a strategic position in the centre of each half-channel cavity Sazanov, As in complex I, these key residues are connected by additional polar residues and form a central hydrophilic axis running through the middle of the membrane across the entire complex Figure 4a,b. Waters predicted in Dowser software are shown as red spheres and the hydrogen bonds involving protonatable residues and waters are shown as black dashes.

Distances for important electrostatic interactions with E a , E d and K d are also indicated. Side-chains of additional polar residues lining the path are shown as thin sticks. Key charged residues along the path are shown as thick sticks and labelled.

Mrp subunits are coloured while complex I subunits are in grey. Where applicable, subunits of T. Transmembrane helices, beta strands and horizontal amphipathic helices are depicted as blue bars above the corresponding sequence. Residues which are involved in proton translocation are depicted with blue asterisks. Interestingly, the bulge appears to be absent in the Mrp, so it may not be a universal feature or it is possible that it may appear in a different state of the complex, for example at high pH current structure is solved at pH 6.

A striking feature of the Mrp complex is the tightly intertwined interface between the two monomers. This shows that the Mrp complex clearly evolved to exist as a dimer in vivo, as also confirmed by the stability of the dimer contacts in all the 3D classes that we observe and the dimer stability during purification in several species Materials and methods and Morino et al.

Another notable feature of the structure is a dramatic tilt of about 35 o of all the TM helices in the small subunits, as compared to MrpA N and MrpD Figure 2d. Such an unusual fold is probably stabilised by the dimer architecture since the helices are tilted in opposite directions at the interface where two protomers meet Figure 1c.

This is obvious from both the hydrophobicity of surface residues and from the calculated surface charge distribution Figure 2a,b. Consistently, the detergent belt, visible in low-resolution maps Figure 2—figure supplement 1h , gets very thin in this area. Overall the exposed hydrophobic belt is roughly linear Figure 2a , consistent with the flatness of lipid bilayer. This suggests that these dimers, with about 20 degrees apparent angle between the monomers, which refined to the highest resolution Figure 1—figure supplement 3 , are probably close to the physiological state of the complex.

These helices are continued in MrpE by a long amphipathic helix AH, Figure 2d , which likely resides at the surface of the membrane Figure 2—figure supplement 1g. This helix is continued by a ferredoxin-fold domain of MrpE, which is exposed to the cytoplasm along with parts of TM helices of MrpG. A very thin hydrophobic belt is clearly unfavourable for membrane protein folding and so it must have a functional role in Mrp, most likely by acting to significantly disturb and thin a lipid membrane in this area.

The thinning of the membrane could be achieved by a combined action of the short MrpE TMH from both monomers Figure 1c driving the long amphipathic helices of MrpE into the bilayer. The highly tilted helices of the small subunits could also help to achieve and sustain the thinning as they approach the dimer interface.

Jimmy Van M

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Try out PMC Labs and tell us what you think. Learn More. Steiner J, Sazanov LA. Structure of the Mrp antiporter complex. Electron Microscopy Data Bank. The mechanism of coupling between ion or electron transfer and proton translocation in this large protein family is unknown. Here, we present the structure of the Mrp complex from Anoxybacillus flavithermus solved by cryo-EM at 3. It is a dimer of seven-subunit protomers with 50 trans-membrane helices each.

proton-call: error: proton.conf does not exist - proton-caller

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Deadly Colorado blaze renews focus on underground coal fires

Skip to search form Skip to main content Skip to account menu You are currently offline. Some features of the site may not work correctly. DOI: Poladyan , G. Kirakosyan , A. Trchounian Published 1 June Chemistry Biophysics The bacterium Enterococcus hirae is able to grow under anaerobic conditions during sugar fermentation pH 8.

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