PDBsum entry 1w0k

Hydrolase

PDB id

1w0k

Contents

			Protein chains

					487 a.a. *


					467 a.a. *


					122 a.a. *

			Ligands

					ADP ×5


					GOL ×3


					PO4

			Metals

					_MG ×5

			Waters ×266

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The structure of bovine f1-Atpase inhibited by ADP and beryllium fluoride.

Authors

R.Kagawa, M.G.Montgomery, K.Braig, A.G.Leslie, J.E.Walker.

Ref.

EMBO J, 2004, 23, 2734-2744. [DOI no: 10.1038/sj.emboj.7600293]

PubMed id

15229653

Abstract

The structure of bovine F1-ATPase inhibited with ADP and beryllium fluoride at 2.0 angstroms resolution contains two ADP.BeF3- complexes mimicking ATP, bound in the catalytic sites of the beta(TP) and beta(DP) subunits. Except for a 1 angstrom shift in the guanidinium of alphaArg373, the conformations of catalytic side chains are very similar in both sites. However, the ordered water molecule that carries out nucleophilic attack on the gamma-phosphate of ATP during hydrolysis is 2.6 angstroms from the beryllium in the beta(DP) subunit and 3.8 angstroms away in the beta(TP) subunit, strongly indicating that the beta(DP) subunit is the catalytically active conformation. In the structure of F1-ATPase with five bound ADP molecules (three in alpha-subunits, one each in the beta(TP) and beta(DP) subunits), which has also been determined, the conformation of alphaArg373 suggests that it senses the presence (or absence) of the gamma-phosphate of ATP. Two catalytic schemes are discussed concerning the various structures of bovine F1-ATPase.



	Figure 3. Figure 3 Superimposition of nucleotide-binding site residues in the [TP] subunits in the structures of bovine ADP-F[1] and BeF[3]^--F[1]. The view is shown in stereo and the ADP-F[1] and BeF[3]^--F[1] structures are coloured and grey, respectively. The [TP]Arg373 side chain adopts dramatically different conformations in the two structures as does [TP]Phe424.		Figure 6. Figure 6 Two possible reaction schemes for ATP hydrolysis by F[1]-ATPase. In parts (A) and (B) F[1]-ATPase is depicted as viewed from the membrane proximal aspect of the intact ATP synthase. For simplicity, only the catalytic -subunits and the centrally located -subunit are shown. ATP^* represents an ATP molecule that is committed to hydrolysis. See text for further details.

Secondary reference #1

Title

Structure of bovine mitochondrial f(1)-Atpase with nucleotide bound to all three catalytic sites: implications for the mechanism of rotary catalysis.

Authors

R.I.Menz, J.E.Walker, A.G.Leslie.

Ref.

Cell, 2001, 106, 331-341. [DOI no: 10.1016/S0092-8674(01)00452-4]

PubMed id

11509182

Full text

Abstract



	Figure 4. Figure 4. A Scheme for the Binding Change Mechanism of Catalysis in F[1]-ATPase at Saturating Concentrations of ATP Based on the Bovine Crystal Structures		Figure 6. Figure 4 Schematic representations of the nucleotide-binding

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #2

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

Full text

Abstract



	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 reproduced from the cited reference with permission from Macmillan Publishers Ltd

Secondary reference #3

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

Full text

Abstract



	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).