BCS1
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BCS1
BCS1 (BSC1L encoded) is a homo-heptameric protein (chain A) that crosses the inner mitochondrial membrane and is involved in the assembly of cytochrome III complex (part of the electron transfer chain), specifically the loading of the Rieske FeS protein in an ATP dependent manner. It also plays a role in the LETM1 complex assembly (involved in mitochondrial tubular networks).
Parts
The protein shown is a model derived from the cryoEM-solved structure of the mouse BCS1 in the ATP bound state (PDB:6UKS), but threaded to human (for code see GitHub). Each monomer is comprised of:
- Residues 1-28 are not resolved in any structure, for simplicity the sequence is shown as a helix, but may be disordered and/or may be a non-standard mitochondrial translocation signal that gets cleaved off.
- Residues 29–49 are a transmembrane helix (30 Å long), shown as straight. In the non-membrane–embedded cyroEM structure 6UKP the helices are bent inwards.
- Residues 50–165 form a BCS1 specific domain
- Residues 166–354 form a RecA-like domain, which along with the helix-bundle domain form a AAA hydrolase and at the interface with another chain ATP is bound.
- Residues 355–418 form a helix bundle involved in the ATP-hydrolase activity, which shifts position on hydrolysis.
Variants
Variants discussed in manuscript in preparation (all):
- p.Asn13Ser (wildtype/mutant/mutant) Residues 2-28 do not match the signature of a canonical mitochondrial translocation signal, but is absent in the density, which may suggest it is either disordered or was cleaved off.
- p.Arg33Gln (wildtype/mutant/mutant) Arginines, being positively charged residues, at the start of a membrane spanning region may bind a phosphate head of the lipid bilayer. Arg33 and Lys34, next to it, are outwards facing positively charged residues in the transmembrane helix close to the intermembrane space. However, this is at odds with the 30 Å inwards tilt and membrane thickness, indicating that these two residues must be binding something and/or distorting the membrane.
- p.Arg45Cys (wildtype/mutant/mutant) Like Arg33 this is a charged residue within the transmembrane helix, but near the edge with the matrix. It is flanked by Arg45 and both face outwards, a helix turn further on, are methionine and tyrosine, the last two hydrophobic residues in the helix. This cannot be a diarginine motif for ER retention as mitochondrial protein are translocated from the cytoplasm, not via the ER.
- p.Arg69Cys (wildtype/mutant/mutant) Destabilising due to loss of surface salt bridges with Glu96 on a nearby sheet in the Apo structure only (+6 kcal/mol for apo, 2 kcal/mol for ATP-bound).
- p.Ser78Gly (wildtype/mutant/mutant) Ser78 hydrogen bonds with Arg117 forming the core of the domain, this loss of bonding (+6 kcal/mol) is compensated by better backbone torsions (-5 kcal/mol), but weakens the interface with a nearby chain (+2 kcal/mol).
- p.Pro99Leu (wildtype/mutant/mutant) Pro99 is at the end of a sheet and before a turn, the mutation is deleterious (+7–9 kcal/mol), but due to clashes and not torsion.
- p.Arg109Trp (wildtype/mutant/mutant) Arg109 forms a surface salt-bridge to Glu153. The change to a bulky hydrophobic residue is predicted to be destabilising (+6–7 kcal/mol) due to electrostatic and steric clashes.
- p.Gly129Arg (wildtype/mutant/mutant) Hydrogen donor residue of a β-turn with Leu126. Highly destabilising for the apo-form (+10 kcal/mol) due to several steric clashes (Pauli repulsion forces) , which also affect interchain binding (+3 kcal/mol).
- p.Thr138Met (wildtype/mutant/mutant) The mutation on this sheet residue is predicted to be destabilising (+3 kcal/mol) in the apo-form due to some steric clashes, which also affect interchain binding (+2 kcal/mol, both).
- p.Arg155Gln (wildtype/mutant/mutant) Arg155 founds a salt-bridge with the next residue along in the helix, Glu156, and the lower half of the sidechain interacts with another chain. This is predicted to be destabilising (+4–5 kcal/mol) due to steric clashes and worse hydrogen bonding.
- p.Glu163Lys (wildtype/mutant/mutant) Glu163 forms a salt bridge with Arg184. Overall it is predicted to be energetically neutral but with a large trade off of worse electrostatic clashes with improved backbone torsions (similarly to Arg183His).
- p.Arg183His (wildtype/mutant/mutant) This residue is part of a four arginine repeat (unusual), which form various salt bridges, but are out of binding distance to the magnesium. This is predicted to be energetically neutral, but there is a large trade off of worse electrostatic clashes with improved backbone torsions (similarly to Glu163Lys).
- p.Gly230Arg (wildtype/mutant/mutant) This residue disrupts the active site (over +20 kcal/mol), likely abolishing the ATP hydrolysis.
- p.Cys252Tyr (wildtype/mutant/mutant) The mutation of a small residue in the core of the RacA-like domain to a larger one is highly destabilising (over 20 kcal/mol).
- p.Leu307Phe (wildtype/mutant/mutant) This residue in a mobile loop that is likely close to the active site (modelled loop: 14 Å away and buried). This region shift significantly during translocation. With the loop added, it is highly deleterious (+11 kcal/mol).
- p.Leu417Pro (wildtype/mutant/mutant) The last three residues are Leu-Arg-Arg and are structural in the ATP-form. The leucine sidechain is structural and the terminal Arg419 forms a salt-bridge, hence the over +20 kcal/mol shift in free energy.