PDBsum entry 1d8s

Hydrolase

PDB id: 1d8s

Contents

Protein chains

(+ 0 more) 487 a.a.

214 a.a.

PDB id:

1d8s

Name:

Hydrolase

Title:

Escherichia coli f1 atpase

Structure:

F1 atpase (alpha subunit). Chain: a, b, c. Engineered: yes. F1 atpase (beta subunit). Chain: d, e, f. Engineered: yes. F1 atpase (gamma subunit). Chain: g. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Heptamer (from PQS)

Resolution:

4.40Å R-factor: 0.404

Authors:

A.C.Hausrath,G.Gruber,B.W.Matthews,R.A.Capaldi

Key ref:

A.C.Hausrath et al. (1999). Structural features of the gamma subunit of the Escherichia coli F(1) ATPase revealed by a 4.4-A resolution map obtained by x-ray crystallography. Proc Natl Acad Sci U S A, 96, 13697-13702. PubMed id: 10570135 DOI: 10.1073/pnas.96.24.13697

Date:

25-Oct-99 Release date: 03-Dec-99

Protein chains

No UniProt id for this chain

Struc: 487 a.a.

Protein chain

No UniProt id for this chain

Struc: 214 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G: E.C.3.6.1.34 - Transferred entry: 7.1.2.2.

DOI no: 10.1073/pnas.96.24.13697

Proc Natl Acad Sci U S A 96:13697-13702 (1999)

PubMed id: 10570135

Structural features of the gamma subunit of the Escherichia coli F(1) ATPase revealed by a 4.4-A resolution map obtained by x-ray crystallography.

A.C.Hausrath, G.Grüber, B.W.Matthews, R.A.Capaldi.

ABSTRACT

The F(1) part of the F(1)F(O) ATP synthase from Escherichia coli has been crystallized and its structure determined to 4.4-A resolution by using molecular replacement based on the structure of the beef-heart mitochondrial enzyme. The bacterial F(1) consists of five subunits with stoichiometry alpha(3), beta(3), gamma, delta, and epsilon. delta was removed before crystallization. In agreement with the structure of the beef-heart mitochondrial enzyme, although not that from rat liver, the present study suggests that the alpha and beta subunits are arranged in a hexagonal barrel but depart from exact 3-fold symmetry. In the structures of both beef heart and rat-liver mitochondrial F(1), less than half of the structure of the gamma subunit was seen because of presumed disorder in the crystals. The present electron-density map includes a number of rod-shaped features which appear to correspond to additional alpha-helical regions within the gamma subunit. These suggest that the gamma subunit traverses the full length of the stalk that links the F(1) and F(O) parts and makes significant contacts with the c subunit ring of F(O).

Selected figure(s)

Figure 2.
Fig. 2. (a) Electron-density map for ECF[1]. As discussed in the text, the backbone atoms of the [3] [3] hexamer, as seen in the structure of the beef-heart mitochondrial enzyme (10), were placed in the E. coli unit cell by molecular replacement and then used to calculate phases, which were used to calculate the map shown. The coefficients are (F[o]-F[c]), where the F[o] are the amplitudes observed for the ECF[1] crystals, and the F[c] are the structure factors calculated from the backbone atoms of the [3] [3] hexamer. The C^ backbones of the and subunits are shown in blue and green, respectively. [In the nomenclature of Abrahams et al. (10), these are, respectively, the [E] and [TP] subunits.] The resolution of the map is 4.4 Å, and it is contoured at 2.0 , where is the root-mean-square density throughout the unit cell. The strongest features in the map consist of a series of rods, suggesting -helices. (b) Electron-density map, as in a, with the backbone of part of the subunit, as seen in the structure of beef-heart MF[1] superimposed in red. was placed by superimposing the [3] [3] backbone atoms of MF[1] and ECF[1] and applying the same transformation to the MF[1] subunit. As is apparent in the figure, the electron density for the E. coli enzyme corresponds remarkably well with the -helical coiled-coil of the subunit, which lies at the center of the [3] [3] hexamer and extends below. The present map shows that the two -helices within the coiled-coil extend several turns beyond the point at which they can no longer be seen in the structure of beef-heart MF[1]. (The rod of density labeled G extends beyond that seen in this figure but lies outside the field of view.) Another -helix, including residues 77-90 of the subunit, was seen in the bovine MF[1] structure close to the so-called DELSEED region of the subunit. This helix is also shown in red and coincides with rod-like electron density labeled C. Additional rod-like density features seen at the bottom of the figure, including that labeled B, are presumed to correspond to other -helices of the subunit. The features labeled A', G', and B' are related by symmetry to A, G, and B and are associated with an adjacent molecule in the crystal. Similarly, the feature T' is also associated with another molecule in the crystal. The density is in the vicinity of the 25 or so amino-terminal residues that are at the "top" of the subunit and are not seen in the structure of beef-heart MF[1] (10). The presence of this density feature may indicate that some of these residues are better ordered in the present crystal form. The electron-density features that are within the region occupied by the and subunits are presumed to reflect the fact that the observed structure factors, F[o], come from the intact ECF[1] particle, whereas the calculated structure factors, F[c], include only the polyglycine backbone atoms of the and

Figure 4.
Fig. 4. (Left) Ribbon drawings showing two views, at right angles, of the structure of the [3] [3] subunits of ECF[1] as seen in the present 4.4-Å resolution electron-density map. (Right) Electron micrographs of intact ECF[1]F[O] [reprinted with permission from S. Wilkens and R. A. Capaldi and reproduced with permission from ref. 7 (Copyright 1998, Nature). In the top view, the main connection between the [3] [3] hexamer and the c-ring is assumed to be made by the and subunits (Fig. 1). There is also thought to be a second connection, at the extreme left of the figure, made by the two b subunits. In the bottom view, the particle is rotated roughly 90°.

Figures were selected by an automated process.