H+-transporting two-sector ATPase (F-type, bacterial)

 

The F0 subunit of E.coli ATP synthase is involved in proton translocation across the membrane from the periplasm to the cytoplasm. Structurally it shows a high degree of similarity to the mitochondrial and cytoplasmic versions of the enzyme, indicating that a common mechanism of ATP synthesis is used by all. The ATP synthase can also function in the reverse direction, where ATP hydrolysis by the F1 (soluble) subunit is coupled to movement of protons across the membrane against the concentration gradient rather than with it. The components of the ATP synthase F0 subunit are one a, 2 b and 12 c units which interact together to allow rotation to occur, driving ATP synthesis.

 

Reference Protein and Structure

Sequences
P68699 UniProt
P0AB98 UniProt IPR000568 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1c17 - A1C12 SUBCOMPLEX OF F1FO ATP SYNTHASE (solution nmr Å) PDBe PDBsum 1c17
Catalytic CATH Domains
1.20.20.10 CATHdb 1.20.120.220 CATHdb (see all for 1c17)
Click To Show Structure

Enzyme Reaction (EC:7.1.2.2)

ATP(4-)
CHEBI:30616ChEBI
+
hydron
CHEBI:15378ChEBI
+
water
CHEBI:15377ChEBI
→
ADP(3-)
CHEBI:456216ChEBI
+
hydron
CHEBI:15378ChEBI
+
hydrogenphosphate
CHEBI:43474ChEBI
Alternative enzyme names: ATP synthase, F(1)-ATPase, F(o)F(1)-ATPase, H(+)-transporting ATPase, Bacterial Ca(2+)/Mg(2+) ATPase, Chloroplast ATPase, Coupling factors (F(o), F(1) and CF(1)), Mitochondrial ATPase, F(0)F(1)-ATPase, H(+)-transporting ATP synthase,

Enzyme Mechanism

Introduction

The synthesis of ATP occurs through proton translocation across the membrane. A proton is picked up by Asn 214 on the periplasmic side where the H+ concentration is high. This is then passed to Asp 61, causing the breaking of a salt bridge between this residue and Arg 210. As a result, the Asp 61 residue moves away from the Arg 210, causing the helix to move with it and the rotation of around 30 degrees relative to the a domain which leads to conformational changes in the F1 subunit and consequential ATP synthesis. The proton is passed from Asp 61 to the cytoplasm via Ser 206, so that the Asp 61 can accept another proton from the periplasm and continue the cycle.

Catalytic Residues Roles

UniProt PDB* (1c17)
Asn214 Asn214(120)M Picks up proton from periplasmic side of the ATP synthase and passes it to Asp 61 to cause conformational change. proton acceptor
Ser206 Ser206(112)M Picks up proton from Asp 61 and transfers it to the cytoplasmic side of the ATP synthase, thus allowing Asp 61 to return to its original position. proton relay, proton acceptor, proton donor
Asp61 Asp61L Accepts proton causing the change in the salt bridge with Arg 210 that results in rotation of the c subcomplex and the consequential conformational change that leads to ATP synthesis. proton acceptor, electrostatic stabiliser, proton donor
Arg210 Arg210(116)M By forming a salt bridge to the deprotonated form of Asp 61, modifies the pKa such that protonation results in the breaking of this salt bridge and the rotation of the c subcomplex relative to the a subcomplex. electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, overall reactant used, native state of enzyme regenerated, overall product formed

References

  1. Dmitriev OY et al. (2002), Biochemistry, 41, 5537-5547. Structure of Ala24/Asp61 → Asp24/Asn61 Substituted SubunitcofEscherichia coliATP Synthase:  Implications for the Mechanism of Proton Transport and Rotary Movement in the FoComplex†. DOI:10.1021/bi012198l. PMID:11969414.
  2. Mashkovtseva E et al. (2013), Math Biosci, 243, 117-125. Combined mathematical methods in the description of the F(o)F(1)-ATP synthase catalytic cycle. DOI:10.1016/j.mbs.2013.02.013. PMID:23499574.
  3. Mukherjee S et al. (2012), Proc Natl Acad Sci U S A, 109, 14876-14881. Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase. DOI:10.1073/pnas.1212841109. PMID:22927379.
  4. Aksimentiev A et al. (2004), Biophys J, 86, 1332-1344. Insights into the Molecular Mechanism of Rotation in the Fo Sector of ATP Synthase. DOI:10.1016/s0006-3495(04)74205-8. PMID:14990464.
  5. Rastogi VK et al. (1999), Nature, 402, 263-268. Structural changes linked to proton translocation by subunit c of the ATP synthase. DOI:10.1038/46224. PMID:10580496.
  6. Valiyaveetil FI et al. (1997), J Biol Chem, 272, 32635-32641. On the Role of Arg-210 and Glu-219 of Subunit a in Proton Translocation by the Escherichia coliF0F1-ATP Synthase. DOI:10.1074/jbc.272.51.32635. PMID:9405480.
  7. Kluge C et al. (1993), Biochemistry, 32, 10378-10386. Kinetics of inactivation of the F1F0 ATPase of Propionigenium modestum by dicyclohexylcarbodiimide in relationship to hydrogen ion and sodium concentration: Probing the binding site for the coupling ions. DOI:10.1021/bi00090a013. PMID:8399181.

Step 1. Asn214 (M) accepts a proton from the periplasmic side.

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Catalytic Residues Roles

Residue Roles
Arg210(116)M electrostatic stabiliser
Asp61L electrostatic stabiliser
Asn214(120)M proton acceptor

Chemical Components

proton transfer, overall reactant used

Step 2. Asp 61 (L) accepts a proton from Asn 214 (M) which results in the breaking of a salt bridge between this residue and Arg 210. As a result, the Asp 61 residue moves away from the Arg 210, causing the helix to move with it and the rotation of around 30 degrees relative to the a domain.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Arg210(116)M electrostatic stabiliser
Asp61L proton acceptor

Chemical Components

proton transfer

Step 3. The proton is transferred from Asp 61 (L) to Ser 206 (M) which then releases a proton into the cytoplasm. As result the helix containing Asp 61 (M) rotates back to its original conformation so that it is ready to receive another proton.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Arg210(116)M electrostatic stabiliser
Asp61L proton donor
Ser206(112)M proton donor, proton acceptor, proton relay

Chemical Components

proton transfer, native state of enzyme regenerated, overall product formed
Download: Image, Marvin File

Step 1. Asn214 (M) accepts a proton from the periplasmic side.

Step 2. Asp 61 (L) accepts a proton from Asn 214 (M) which results in the breaking of a salt bridge between this residue and Arg 210. As a result, the Asp 61 residue moves away from the Arg 210, causing the helix to move with it and the rotation of around 30 degrees relative to the a domain.

Step 3. The proton is transferred from Asp 61 (L) to Ser 206 (M) which then releases a proton into the cytoplasm. As result the helix containing Asp 61 (M) rotates back to its original conformation so that it is ready to receive another proton.

Products.

Contributors

Peter Sarkies, Gemma L. Holliday, Charity Hornby