PDBsum entry 2f43

Hydrolase

PDB id: 2f43

Contents

Protein chains

480 a.a. *

471 a.a. *

124 a.a. *

Ligands

ATP

VO4

ADP

Metals

_MG ×2

* Residue conservation analysis

PDB id:

2f43

Name:

Hydrolase

Title:

Rat liver f1-atpase

Structure:

Atp synthase alpha chain, mitochondrial. Chain: a. Atp synthase beta chain, mitochondrial. Chain: b. Atp synthase gamma chain, mitochondrial. Chain: g. Ec: 3.6.3.14

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Organ: liver. Organ: liver

Biol. unit:

Heptamer (from PDB file)

Resolution:

3.00Å R-factor: 0.306 R-free: 0.320

Authors:

C.Chen,A.K.Saxena,W.N.Simcoke,D.N.Garboczi,P.L.Pedersen,Y.H.Ko

Key ref:

C.Chen et al. (2006). Mitochondrial ATP synthase. Crystal structure of the catalytic F1 unit in a vanadate-induced transition-like state and implications for mechanism. J Biol Chem, 281, 13777-13783. PubMed id: 16531409 DOI: 10.1074/jbc.M513369200

Date:

22-Nov-05 Release date: 07-Mar-06

Protein chain

P15999  (ATPA_RAT) -  ATP synthase subunit alpha, mitochondrial from Rattus norvegicus

Seq: 553 a.a.

Struc: 480 a.a.

Protein chain

P10719  (ATPB_RAT) -  ATP synthase subunit beta, mitochondrial from Rattus norvegicus

Seq: 529 a.a.

Struc: 471 a.a.

Protein chain

P35435  (ATPG_RAT) -  ATP synthase subunit gamma, mitochondrial from Rattus norvegicus

Seq: 273 a.a.

Struc: 124 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, G: E.C.3.6.3.14 - Transferred entry: 7.1.2.2.
• Reaction: ATP + H₂O + H⁺(In) = ADP + phosphate + H⁺(Out)

ATP + H(2)O + H(+)(In) = ADP (Bound ligand (Het Group name = ATP) matches with 87.10% similarity) + phosphate + H(+)(Out)

• Enzyme class 2: Chain B: E.C.7.1.2.2 - H(+)-transporting two-sector ATPase.
• Reaction: ATP + H2O + 4 H⁺(in) = ADP + phosphate + 5 H⁺(out)

ATP (Bound ligand (Het Group name = ATP) corresponds exactly) + H2O + 4 × H(+)(in) = ADP + phosphate + 5 × H(+)(out)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M513369200

J Biol Chem 281:13777-13783 (2006)

PubMed id: 16531409

Mitochondrial ATP synthase. Crystal structure of the catalytic F1 unit in a vanadate-induced transition-like state and implications for mechanism.

C.Chen, A.K.Saxena, W.N.Simcoke, D.N.Garboczi, P.L.Pedersen, Y.H.Ko.

ABSTRACT

ATP synthesis from ADP, P(i), and Mg2+ takes place in mitochondria on the catalytic F1 unit (alpha3beta3gammedeltaepsilon) of the ATP synthase complex (F0F1), a remarkable nanomachine that interconverts electrochemical and mechanical energy, producing the high energy terminal bond of ATP. In currently available structural models of F1, the P-loop (amino acid residues 156GGAGVGKT163) contributes to substrate binding at the subunit catalytic sites. Here, we report the first transition state-like structure of F1 (ADP.V(i).Mg.F1) from rat liver that was crystallized with the phosphate (P(i)) analog vanadate (VO(3-)4 or V(i)). Compared with earlier "ground state" structures, this new F1 structure reveals that the active site region has undergone significant remodeling. P-loop residue alanine 158 is located much closer to V(i) than it is to P(i) in a previous structural model. No significant movements of P-loop residues of the subunit were observed at its analogous but noncatalytic sites. Under physiological conditions, such active site remodeling involving the small hydrophobic alanine residue may promote ATP synthesis by lowering the local dielectric constant, thus facilitating the dehydration of ADP and P(i). This new crystallographic study provides strong support for the catalytic mechanism of ATP synthesis deduced from earlier biochemical studies of liver F1 conducted in the presence of V(i) (Ko, Y. H., Bianchet, M., Amzel, L. M., and Pedersen, P. L. (1997) J. Biol. Chem. 272, 18875-18881; Ko, Y. H., Hong, S., and Pedersen, P. L. (1999) J. Biol. Chem. 274, 28853-28856).

Selected figure(s)

Figure 4.
FIGURE 4. A, plot of the difference in distance between -subunit atoms in the ADP·V[i]·Mg·F[1] transition state-like structure reported here aligned with the corresponding -subunit atoms of the ADP·P[i]·F[1] structure (10). The two -subunit structures were aligned and the average distance between corresponding amino acid atoms at each position throughout the sequences (residues 1-399 and 406-477) were calculated and plotted against residue number. The average distance that includes all difference calculations between all corresponding atoms in the two structures is only 0.36 Å. In contrast, difference calculations between corresponding atoms in the two structures that include the P-loop (^156GGAGVGKT^163) gave an average value of 1.0 Å (red line). B, overlay of a stick representation of the P-loop region of the subunit of the ADP·V[i]·Mg·F[1] transition state-like structure reported here with that of the subunit of the ADP·P[i]·F[1] structure (10). The conformational differences in the P-loops of the two structures are clearly delineated as are the relative positions of the -carbon atom of Ala^158. In addition, the overlay shows that V[i] (red) is much nearer the P-loop in the ADP·V[i]·Mg·F[1] structure than is P[i] (green)in the ADP·P[i]·F[1] structure.

Figure 7.
FIGURE 7. Proposed critical events in the formation of ATP catalyzed by the F[1] moiety of mitochondrial ATP synthase based on structural work reported here, our earlier collaborative structural studies (10), and our earlier biochemical studies (15, 16). In the top, ADP and P[i] are both able to bind to the catalytic F[1] moiety of rat liver ATP synthase in the absence of Mg^2+ (10). In the middle, when Mg^2+ enters it binds to the bound P[i], facilitating the formation of the transition state (16). ADP and MgP[i] are then brought closer together, whereas the methyl group of P-loop alanine 158 is brought into the active site. The lower dielectric environment facilitates the release of water as the ADP and MgP[i] are dehydrated to form ATPMg (bottom).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 13777-13783) copyright 2006.

Figures were selected by an automated process.