PDBsum entry 1e79

Hydrolase

PDB id: 1e79

Contents

Protein chains

492 a.a. *

467 a.a. *

263 a.a. *

131 a.a. *

47 a.a. *

Ligands

ATP ×2

ADP ×3

GOL

DCW

SO4

Metals

_MG ×5

Waters ×911

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The structure of the central stalk in bovine f(1)-Atpase at 2.4 a resolution.

Authors

C.Gibbons, M.G.Montgomery, A.G.Leslie, J.E.Walker.

Ref.

Nat Struct Biol, 2000, 7, 1055-1061. [DOI no: 10.1038/80981]

PubMed id

11062563

Abstract

The central stalk in ATP synthase, made of gamma, delta and epsilon subunits in the mitochondrial enzyme, is the key rotary element in the enzyme's catalytic mechanism. The gamma subunit penetrates the catalytic (alpha beta)(3) domain and protrudes beneath it, interacting with a ring of c subunits in the membrane that drives rotation of the stalk during ATP synthesis. In other crystals of F(1)-ATPase, the protrusion was disordered, but with crystals of F(1)-ATPase inhibited with dicyclohexylcarbodiimide, the complete structure was revealed. The delta and epsilon subunits interact with a Rossmann fold in the gamma subunit, forming a foot. In ATP synthase, this foot interacts with the c-ring and couples the transmembrane proton motive force to catalysis in the (alpha beta)(3) domain.

Figure 2.
Figure 2. The structure of the central stalk. The color code for subunits is the same as in Fig. 1. The light blue regions have been described in earlier structures and new regions of structure in the subunit are dark blue. a, Side-on stereo view of stalk subunits (same view as in Fig. 1a). b, Stereo view of stalk subunits, rotated 90° with respect to ( a), viewed from the membrane.

Figure 5.
Figure 5. Interaction of gamma Arg 75 with residues in the and subunits to form part of the catalytic 'catch'. Distances are in Å.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2000, 7, 1055-1061) copyright 2000.

Secondary reference #1

Title

Molecular architecture of the rotary motor in ATP synthase.

Authors

D.Stock, A.G.Leslie, J.E.Walker.

Ref.

Science, 1999, 286, 1700-1705. [DOI no: 10.1126/science.286.5445.1700]

PubMed id

10576729

Figure 2.
Fig. 2. Stereo views of an electron density map of the yeast F[1]c[10] complex. The solvent flattened map was calculated at 3.9 Å resolution and contoured at 1.5 . (A) Side view containing the bovine F[1] C model (with in orange, in yellow, and in green). The density of symmetry-related molecules in the crystal is masked out. The inset indicates the location of the subunits within the complex. The location of the section shown in (C) is indicated by the white box; the direction of the view is indicated by the arrow. The presumed membrane region (M) (2) is marked by the two dotted lines. The c subunits are numbered 3, 2, 1, 10, and 9 (the best ordered c subunit was chosen as number 1). The overall height of the complex is ~190 Å, of which the [3] [3] subcomplex accounts for 83 Å, the stalk for 50 Å, and the c subunits for 58 Å. (B) Enlarged view of the / -c contact region with the model (and numbering) of the E. coli subunit (in red) and the E. coli c subunit (in white) fitted into the density, contoured at 1.0 . The white box in the inset indicates the location of the displayed section within the complex. (C) End-on view of the density of the c ring. The inset shows the location of the , , , and subunits in relation to the c subunits. The helices of the c subunit are drawn as blue circles, the larger outer circles accounting for the larger side chains in the COOH-terminal helix. The outer diameter of the c ring is 55 Å (top) to 42 Å (equator) to 45 Å (bottom), and the inner diameter is 27 Å (top) to 17 Å (equator) to 22 Å (bottom). The dimensions exclude consideration of unresolved regions of density, including amino acid side chains and detergent or lipid molecules. The two regions of density near subunit 10 are not extensive and are likely to be noise.

Figure 3.
Fig. 3. Stereo view of the crystal packing of the yeast F[1]c[10] complex. A 45 Å thick section through the crystal perpendicular to the crystallographic y axis is shown. The electron density is contoured at 1.2 . The red lines mark the x and z axes of the crystal lattice. All figures were prepared with the program MAIN (72).

The above figures are reproduced from the cited reference with permission from the AAAs

Secondary reference #2

Title

Atp synthesis by rotary catalysis (nobel lecture)

Author

J.E.Walker.

Ref.

angewandte, 1998, 37, 2309.

Secondary reference #3

Title

Crystal structure of the epsilon subunit of the proton-Translocating ATP synthase from escherichia coli.

Authors

U.Uhlin, G.B.Cox, J.M.Guss.

Ref.

Structure, 1997, 5, 1219-1230. [DOI no: 10.1016/S0969-2126(97)00272-4]

PubMed id

9331422

Figure 1.
Figure 1. The structure of the E. coli ATP synthase epsilon, Greek subunit. (a) Stereo diagram of the Ca trace with residue numbers highlighting specific points mentioned in the text. The colours indicate average B factor values for each residue with the lowest values in blue and the highest in red. (b) Structure of the protein with arrows representing b sheets and coils representing a helices. Colours are ramped from the N terminus in blue to the C terminus in red. (The figure was prepared using the programs O [28] and MOLSCRIPT [42].) (c) Topology diagram showing b sheets as arrows and a helices as cylinders. The first and last residues of each secondary structure element are numbered; the N and C termini are marked.

The above figure is reproduced from the cited reference with permission from Cell Press

Secondary reference #4

Title

Structure at 2.8 a resolution of f1-Atpase from bovine heart mitochondria.

Authors

J.P.Abrahams, A.G.Leslie, R.Lutter, J.E.Walker.

Ref.

Nature, 1994, 370, 621-628.

PubMed id

8065448

Secondary reference #5

Title

Crystallization of f1-Atpase from bovine heart mitochondria.

Authors

R.Lutter, J.P.Abrahams, M.J.Van raaij, R.J.Todd, T.Lundqvist, S.K.Buchanan, A.G.Leslie, J.E.Walker.

Ref.

J Mol Biol, 1993, 229, 787-790.

PubMed id

8433373

Secondary reference #6

Title

Inactivation of the bovine mitochondrial f1-Atpase with dicyclohexyl[14c]carbodiimide leads to the modification of a specific glutamic acid residue in the beta subunit.

Authors

F.S.Esch, P.Böhlen, A.S.Otsuka, M.Yoshida, W.S.Allison.

Ref.

J Biol Chem, 1981, 256, 9084-9089.

PubMed id

6114957